allen mouse brain connectivity atlas - allen brain...

117
MARCH 2016 v.9 alleninstitute.org Injection Sites and Stereotaxic Coordinates brain-map.org page 1 of 117 Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER: INJECTION SITES AND STEREOTAXIC COORDINATES FOR ANTEROGRADE PROJECTOME (BRAIN-WIDE) Table 1. Stereotaxic coordinates used for axonal projection mapping study (excluding ISI-directed visual area injections). Brain region (primary structure infected by rAAV) Reference atlas acronym Mouse strain Experiment ID AP ML DV Angle° Abducens nucleus VI Chat-IRES-Cre 168616111 -5.52 0.50 3.75 0 Accessory olfactory bulb AOB C57BL/6J 120812686 3.20 1.00 1.40 0 Accessory olfactory bulb AOB C57BL/6J 272918345 3.70 1.50 0.40 0 Accessory olfactory bulb AOB Cdhr1-Cre_KG66 182686228 3.08 1.00 1.75 0 Accessory olfactory bulb AOB Efr3a- Cre_NO108 267760731 2.80 1.25 1.30, 1.67 0 Accessory olfactory bulb AOB Gad2-IRES-Cre 266563321 3.08 1.00 1.75 0 Accessory olfactory bulb AOB Syt17-Cre_NO14 161178152 3.00 1.00 1.50 0 Agranular insular area AI C57BL/6J 112596790 1.78 2.40, 2.80 2.24 0 Agranular insular area AI Chrna2- Cre_OE25 292209592 1.78 2.40, 2.80 2.25 0 Agranular insular area AI Cux2-IRES-Cre 299783689 1.10 3.25 1.9, 2.35 0

Upload: others

Post on 05-Aug-2020

8 views

Category:

Documents


3 download

TRANSCRIPT

Page 1: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 1 of 117

Allen Mouse Brain Connectivity Atlas

TECHNICAL WHITE PAPER: INJECTION SITES AND STEREOTAXIC COORDINATES FOR ANTEROGRADE PROJECTOME (BRAIN-WIDE)

Table 1. Stereotaxic coordinates used for axonal projection mapping study (excluding ISI-directed visual area injections).

Brain region (primary structure infected by rAAV)

Reference atlas acronym

Mouse strain Experiment ID AP ML DV Angle°

Abducens nucleus VI Chat-IRES-Cre 168616111 -5.52 0.50 3.75 0

Accessory olfactory bulb AOB C57BL/6J 120812686 3.20 1.00 1.40 0

Accessory olfactory bulb AOB C57BL/6J 272918345 3.70 1.50 0.40 0

Accessory olfactory bulb AOB Cdhr1-Cre_KG66 182686228 3.08 1.00 1.75 0

Accessory olfactory bulb AOB Efr3a-Cre_NO108

267760731 2.80 1.25 1.30, 1.67

0

Accessory olfactory bulb AOB Gad2-IRES-Cre 266563321 3.08 1.00 1.75 0

Accessory olfactory bulb AOB Syt17-Cre_NO14 161178152 3.00 1.00 1.50 0

Agranular insular area AI C57BL/6J 112596790 1.78 2.40, 2.80 2.24 0

Agranular insular area AI Chrna2-Cre_OE25

292209592 1.78 2.40, 2.80 2.25 0

Agranular insular area AI Cux2-IRES-Cre 299783689 1.10 3.25 1.9, 2.35

0

Page 2: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 2 of 117

Agranular insular area AI Htr2a-Cre_KM207

262536037 1.78 2.40, 2.80 2.25 0

Agranular insular area AI Rbp4-Cre_KL100 296048512 1.78 2.40, 2.80 2.25 0

Agranular insular area, dorsal part AId A930038C07Rik-Tg1-Cre

267397941 1.78 2.40, 2.80 2.24 0

Agranular insular area, dorsal part AId C57BL/6J 170721670 3.10 1.40 0.65 0

Agranular insular area, dorsal part AId C57BL/6J 180673746 3.10 1.40 0.65 0

Agranular insular area, dorsal part AId C57BL/6J 180709230 2.60 2.00 2.40 0

Agranular insular area, dorsal part AId Glt25d2-Cre_NF107

313327028 1.78 2.40 2.25 0

Agranular insular area, dorsal part AId Grp-Cre_KH288 184168899 1.78 2.80 2.25 0

Agranular insular area, dorsal part AId Ntsr1-Cre_GN220

159322514 1.78 2.40, 2.80 2.24 0

Agranular insular area, dorsal part AId Rbp4-Cre_KL100 166153483 1.78 2.40, 2.80 2.24 0

Agranular insular area, dorsal part AId Syt6-Cre_KI148 264320859 1.78 2.40, 2.80 2.24 0

Agranular insular area, dorsal part AId Tlx3-Cre_PL56 294525229 -4.36 4.25 1.35 0

Agranular insular area, posterior part AIp C57BL/6J 174361746 -0.58 4.00 2.15 0

Agranular insular area, posterior part AIp Chrna2-Cre_OE25

297858011 -0.34 3.85 3.00 0

Agranular insular area, posterior part AIp Cux2-IRES-Cre 272827141 -0.34 4.00, 3.75 3.00 0

Agranular insular area, posterior part AIp Rbp4-Cre_KL100 183330908 -0.34 4.00, 3.75 3.00, 3.25

0

Agranular insular area, posterior part AIp Syt6-Cre_KI148 168095756 -0.34 4.00, 3.75 3.00, 3.25

0

Anterior amygdalar area AAA Adcyap1-2A-Cre 187269162 -0.46 2.20 5.22 0

Anterior amygdalar area AAA C57BL/6J 159650350 0.14 2.10 4.80 0

Anterior amygdalar area AAA C57BL/6J 175372863 -0.30 2.12 4.95 0

Page 3: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 3 of 117

Anterior amygdalar area AAA Gad2-IRES-Cre 299245589 -0.30 2.00 4.85 0

Anterior amygdalar area AAA Rbp4-Cre_KL100 300641829 -0.46 2.20 5.22 0

Anterior cingulate area ACA Efr3a-Cre_NO108

267749107 0.26 0.25 1.25 0

Anterior cingulate area ACA Gpr26-Cre_KO250

265712971 0.26 0.25 1.25 0

Anterior cingulate area ACA Gpr26-Cre_KO250

287248684 1.10 0.25 0.85 0

Anterior cingulate area ACA Grp-Cre_KH288 265291552 0.26 0.25 1.25 0

Anterior cingulate area ACA Htr2a-Cre_KM207

287714903 1.10 0.25 1.30 0

Anterior cingulate area ACA Ntsr1-Cre_GN220

266412788 0.26 0.50 1.43 0

Anterior cingulate area ACA Scnn1a-Tg3-Cre 268038262 0.26 0.25 1.25 0

Anterior cingulate area ACA Syt6-Cre_KI148 299829892 1.10 0.25 1.30 0

Anterior cingulate area, dorsal part ACAd A930038C07Rik-Tg1-Cre

166323896 1.10 0.25 1.00 0

Anterior cingulate area, dorsal part ACAd A930038C07Rik-Tg1-Cre

171275617 0.26 0.27 0.80 0

Anterior cingulate area, dorsal part ACAd A930038C07Rik-Tg1-Cre

286774770 1.00 0.75 0.30, 0.75

0

Anterior cingulate area, dorsal part ACAd C57BL/6J 112458114 1.10 0.25 1.00 0

Anterior cingulate area, dorsal part ACAd C57BL/6J 139426984 0.26 0.27 0.80 0

Anterior cingulate area, dorsal part ACAd C57BL/6J 146593590 0.14 0.70 0.40, 0.80

0

Anterior cingulate area, dorsal part ACAd Calb2-IRES-Cre 175719341 0.26 0.27 0.80 0

Anterior cingulate area, dorsal part ACAd Chrna2-Cre_OE25

278069982 0.26 0.27 0.60 0

Page 4: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 4 of 117

Anterior cingulate area, dorsal part ACAd Chrna2-Cre_OE25

292125472 1.10 0.25 0.85 0

Anterior cingulate area, dorsal part ACAd Cort-T2A-Cre 165644051 0.26 0.27 0.80 0

Anterior cingulate area, dorsal part ACAd Crh-IRES-Cre (BL)

183104511 0.26 0.27 0.60 0

Anterior cingulate area, dorsal part ACAd Cux2-IRES-Cre 182338356 1.10 0.25 0.85 0

Anterior cingulate area, dorsal part ACAd Cux2-IRES-Cre 183461297 0.26 0.27 0.60 0

Anterior cingulate area, dorsal part ACAd Efr3a-Cre_NO108

267705378 0.26 0.27 0.60 0

Anterior cingulate area, dorsal part ACAd Efr3a-Cre_NO108

277908168 1.10 0.25 0.85 0

Anterior cingulate area, dorsal part ACAd Erbb4-2A-CreERT2

156742543 0.26 0.27 0.80 0

Anterior cingulate area, dorsal part ACAd Erbb4-2A-CreERT2

182183683 0.26 0.27 0.80 0

Anterior cingulate area, dorsal part ACAd Etv1-CreERT2 114428632 1.10 0.25 1.00 0

Anterior cingulate area, dorsal part ACAd Etv1-CreERT2 181858761 0.26 0.27 0.80 0

Anterior cingulate area, dorsal part ACAd Gad2-IRES-Cre 167512351 0.26 0.27 0.80 0

Anterior cingulate area, dorsal part ACAd Gng7-Cre_KH71 158018630 0.25 0.27 0.80 0

Anterior cingulate area, dorsal part ACAd Grp-Cre_KH288 183472596 1.10 0.25 0.85 0

Anterior cingulate area, dorsal part ACAd Grp-Cre_KH288 184169615 2.10 0.75 0.35, 0.75

0

Anterior cingulate area, dorsal part ACAd Htr2a-Cre_KM207

183618139 2.10 0.75 0.35, 0.75

0

Anterior cingulate area, dorsal part ACAd Htr3a-Cre_NO152

305525773 0.26 0.27 0.60 0

Anterior cingulate area, dorsal part ACAd Ntsr1-Cre_GN220

181179335 0.26 0.50 0.95 0

Page 5: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 5 of 117

Anterior cingulate area, dorsal part ACAd Ntsr1-Cre_GN220

266964075 2.10 0.75 0.35, 0.75

0

Anterior cingulate area, dorsal part ACAd Pvalb-IRES-Cre 168401109 0.26 0.27 0.80 0

Anterior cingulate area, dorsal part ACAd Rbp4-Cre_KL100 125833030 0.26 0.27 0.80 0

Anterior cingulate area, dorsal part ACAd Rbp4-Cre_KL100 161458737 1.10 0.25 1.00 0

Anterior cingulate area, dorsal part ACAd Scnn1a-Tg3-Cre 267101850 0.26 0.27 0.60 0

Anterior cingulate area, dorsal part ACAd Scnn1a-Tg3-Cre 268039675 1.10 0.25 0.85 0

Anterior cingulate area, dorsal part ACAd Sst-IRES-Cre 288262635 0.26 0.27 0.60 0

Anterior cingulate area, dorsal part ACAd Syt6-Cre_KI148 177783204 0.26 0.27 0.60 0

Anterior cingulate area, dorsal part ACAd Tac1-IRES2-Cre 286646877 0.26 0.27 0.60 0

Anterior cingulate area, dorsal part ACAd Trib2-2A-CreERT2

287599685 0.26 0.27 0.60 0

Anterior cingulate area, ventral part ACAv A930038C07Rik-Tg1-Cre

159319654 0.26 0.25 1.25 0

Anterior cingulate area, ventral part ACAv A930038C07Rik-Tg1-Cre

298797288 1.10 0.25 1.30 0

Anterior cingulate area, ventral part ACAv C57BL/6J 112514202 1.10 0.25 1.30 0

Anterior cingulate area, ventral part ACAv C57BL/6J 139520203 0.26 0.25 1.25 0

Anterior cingulate area, ventral part ACAv Chrna2-Cre_OE25

278173743 0.26 0.25 1.25 0

Anterior cingulate area, ventral part ACAv Chrna2-Cre_OE25

299782983 1.10 0.25 1.30 0

Anterior cingulate area, ventral part ACAv Cux2-IRES-Cre 183470468 0.26 0.25 1.25 0

Anterior cingulate area, ventral part ACAv Efr3a-Cre_NO108

301179679 1.10 0.25 1.30 0

Anterior cingulate area, ventral part ACAv Etv1-CreERT2 114475228 0.26 0.25 1.25 0

Anterior cingulate area, ventral part ACAv Grp-Cre_KH288 184213701 1.10 0.25 1.30 0

Page 6: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 6 of 117

Anterior cingulate area, ventral part ACAv Grp-Cre_KH288 265288825 1.34 1.50 0.35, 0.75

0

Anterior cingulate area, ventral part ACAv Ntsr1-Cre_GN220

156546627 0.26 0.25 1.25 0

Anterior cingulate area, ventral part ACAv Rasgrf2-2A-dCre 303783015 0.26 0.25 1.25 0

Anterior cingulate area, ventral part ACAv Rbp4-Cre_KL100 126117554 0.26 0.25 1.25 0

Anterior cingulate area, ventral part ACAv Rbp4-Cre_KL100 286482701 1.10 0.25 1.30 0

Anterior cingulate area, ventral part ACAv Scnn1a-Tg3-Cre 278502708 1.10 0.25 1.30 0

Anterior cingulate area, ventral part ACAv Syt6-Cre_KI148 125801033 0.26 0.25 1.25 0

Anterior cingulate area, ventral part ACAv Syt6-Cre_KI148 126190033 0.26 0.27 0.80 0

Anterior cingulate area, ventral part ACAv Syt6-Cre_KI148 156785529 1.10 0.25 1.00 0

Anterior cingulate area, ventral part ACAv Trib2-2A-CreERT2

287600392 0.26 0.25 1.25 0

Anterior hypothalamic nucleus AHN C57BL/6J 127649713 -0.34 3.00 5.52 30

Anterior hypothalamic nucleus AHN C57BL/6J 127649713 -0.34 3.00 5.52 30

Anterior hypothalamic nucleus AHN C57BL/6J 180674463 -0.58 0.20 4.75 0

Anterior hypothalamic nucleus AHN C57BL/6J 181057754 -0.70 0.40 5.46 0

Anterior hypothalamic nucleus AHN Gad2-IRES-Cre 266490034 -0.46 0.50 4.80 0

Anterior hypothalamic nucleus AHN Gad2-IRES-Cre 300167479 -0.70 0.37 5.50 0

Anterior hypothalamic nucleus AHN Gnrh1-Cre 160399309 0.02 0.25 4.90 0

Anterior hypothalamic nucleus AHN Htr3a-Cre_NO152

305677409 -0.46 1.00 4.88 0

Anterior hypothalamic nucleus AHN Lypd6-Cre_KL156

298049545 -0.46 0.50 5.30 0

Anterior hypothalamic nucleus AHN Sim1-Cre 159375743 -0.46 0.50 4.94 0

Anterior hypothalamic nucleus AHN Sim1-Cre 182842391 -0.58 0.20 4.75 0

Page 7: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 7 of 117

Anterior hypothalamic nucleus AHN Slc17a6-IRES-Cre

292035484 -0.46 0.50 4.80 0

Anterior hypothalamic nucleus AHN Slc18a2-Cre_OZ14

301673462 -0.58 0.20 4.75 0

Anterior olfactory nucleus AON C57BL/6J 113443572 2.96 1.14 2.60 0

Anterior olfactory nucleus AON C57BL/6J 121509711 2.80 0.75 2.60 0

Anterior olfactory nucleus AON Chrna2-Cre_OE25

304719312 2.80 0.75 2.60 0

Anterior olfactory nucleus AON Htr2a-Cre_KM207

287715650 3.08 1.00 3.42 0

Anterior olfactory nucleus AON Slc17a6-IRES-Cre

293546902 3.08 1.00 1.85 0

Anterior olfactory nucleus AON Slc17a7-IRES2-Cre

267103498 2.96 1.14 2.60 0

Anterior olfactory nucleus AON Syt17-Cre_NO14 159994059 2.96 1.14 2.66 0

Anterior olfactory nucleus AON Syt17-Cre_NO14 159994767 2.80 0.75 2.60 0

Anterior olfactory nucleus AON Syt17-Cre_NO14 170949055 2.80 0.75 2.60 0

Anterior olfactory nucleus AON Tac1-IRES2-Cre 294313246 2.96 1.14 2.60 0

Anterior pretectal nucleus APN C57BL/6J 125363160 -2.30 0.80 3.20 0

Anterior pretectal nucleus APN C57BL/6J 127083591 -2.92 1.25 2.76 0

Anterior pretectal nucleus APN C57BL/6J 147789031 -2.80 1.00 2.15 0

Anterior pretectal nucleus APN Efr3a-Cre_NO108

299759175 -3.16 1.60 2.85 0

Anterior pretectal nucleus APN Gad2-IRES-Cre 305235787 -2.70 1.20 2.92 0

Anterior pretectal nucleus APN Grp-Cre_KH288 265293391 -2.92 1.25 2.76 0

Anterior pretectal nucleus APN Slc32a1-IRES-Cre

264076081 -0.70 2.70 2.39 0

Page 8: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 8 of 117

Anterodorsal nucleus AD Slc6a5-Cre_KF109

155735826 -0.70 0.60 2.90 0

Anterodorsal nucleus AD Slc6a5-Cre_KF109

182280916 -0.70 0.60 2.90 0

Anterolateral visual area VISal A930038C07Rik-Tg1-Cre

283017324 -3.40 3.60 0.45 0

Anterolateral visual area VISal C57BL/6J 116903968 -3.40 3.50 0.45 0

Anterolateral visual area VISal C57BL/6J 120437703 -3.08 4.00 0.80 0

Anterolateral visual area VISal C57BL/6J 146858755 -3.40 3.50 0.45 0

Anterolateral visual area VISal Chrna2-Cre_OE25

292174264 -4.16 3.95 0.85 0

Anterolateral visual area VISal Cux2-IRES-Cre 266487079 -3.40 3.60 0.45 0

Anterolateral visual area VISal Cux2-IRES-Cre 287495026 1.70 0.40 2.00 0

Anterolateral visual area VISal Gpr26-Cre_KO250

301210923 -3.40 3.60 0.45 0

Anterolateral visual area VISal Nr5a1-Cre 277849965 -3.40 3.60 0.45 0

Anterolateral visual area VISal Ntsr1-Cre_GN220

287036898 -3.40 3.60 0.45 0

Anterolateral visual area VISal Rbp4-Cre_KL100 167794131 -3.40 3.50 0.45 0

Anterolateral visual area VISal Rorb-IRES2-Cre 298757426 -3.40 3.60 0.45 0

Anterolateral visual area VISal Scnn1a-Tg3-Cre 166459778 -3.40 3.50 0.45 0

Anterolateral visual area VISal Syt6-Cre_KI148 159224478 -3.40 3.50 0.45 0

Anterolateral visual area VISal Syt6-Cre_KI148 292791310 -4.04 4.00 0.35, 0.75

30

Anterolateral visual area VISal Tlx3-Cre_PL56 297225422 -4.04 4.00 0.35, 0.75

30

Anterolateral visual area VISal Tlx3-Cre_PL56 297231636 -3.40 3.60 0.45 0

Page 9: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 9 of 117

Anteromedial nucleus AM C57BL/6J 146658170 -0.46 0.50 3.43 0

Anteromedial nucleus AM C57BL/6J 158840459 -0.34 0.35 3.58 0

Anteromedial nucleus AM Cck-IRES-Cre 159331462 -0.34 0.35 3.58 0

Anteromedial nucleus AM Crh-IRES-Cre (ZJH)

171067319 -0.10 2.55 4.00 30

Anteromedial nucleus AM Grik4-Cre 167571459 -0.58 0.50 3.43 0

Anteromedial nucleus AM Prkcd-GluCla-CFP-IRES-Cre

267610466 -0.58 0.50 3.43 0

Anteromedial nucleus, dorsal part AMd C57BL/6J 146046430 -0.70 0.60 2.90 0

Anteromedial nucleus, dorsal part AMd Gal-Cre_KI87 266174045 -0.58 0.50 3.43 0

Anteromedial visual area VISam A930038C07Rik-Tg1-Cre

298324391 -3.16 1.55 0.17, 0.58

0

Anteromedial visual area VISam C57BL/6J 100141599 -3.16 1.55 0.17, 0.58

0

Anteromedial visual area VISam C57BL/6J 146077302 3.08 1.50 0.40 0

Anteromedial visual area VISam Chrna2-Cre_OE25

297946154 -4.60 3.80 0.45 30

Anteromedial visual area VISam Cux2-IRES-Cre 263780729 -3.80 2.50 0.35 0

Anteromedial visual area VISam Drd3-Cre_KI196 297670312 -2.54 1.75 0.20, 0.55

0

Anteromedial visual area VISam Nos1-CreERT2 308385516 -3.80 2.50 0.35, 0.75

0

Anteromedial visual area VISam Rbp4-Cre_KL100 159753308 -2.54 1.75 0.20, 0.55

0

Anteromedial visual area VISam Rbp4-Cre_KL100 286418177 -3.16 1.55 0.17, 0.58

0

Anteromedial visual area VISam Rbp4-Cre_KL100 294481346 -3.16 1.55 0.17, 0.58

0

Page 10: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 10 of 117

Anteromedial visual area VISam Rorb-IRES2-Cre 301618122 -3.16 1.55 0.17; 0.58

0

Anteromedial visual area VISam Scnn1a-Tg3-Cre 257667830 -3.16 1.55 0.17, 0.58

0

Anteromedial visual area VISam Syt6-Cre_KI148 299733445 -3.16 1.55 0.17, 0.58

0

Anteroventral nucleus of thalamus AV C57BL/6J 114427219 -0.58 1.00 2.93 0

Anteroventral nucleus of thalamus AV Gal-Cre_KI87 175818392 -0.58 1.00 2.93 0

Anteroventral nucleus of thalamus AV Gpr26-Cre_KO250

286553311 -0.58 1.00 2.93 0

Anteroventral nucleus of thalamus AV Grp-Cre_KH288 292478008 -0.58 1.00 2.93 0

Anteroventral nucleus of thalamus AV Slc17a6-IRES-Cre

309702727 -0.82 1.13 3.28 0

Anteroventral periventricular nucleus AVPV C57BL/6J 138059031 0.98 0.25 4.80 0

Anteroventral periventricular nucleus AVPV Kiss1-Cre 299247009 0.50 0.15 4.75 0

Arcuate hypothalamic nucleus ARH Agrp-IRES-Cre 146554676 -1.46 0.10 5.90 0

Arcuate hypothalamic nucleus ARH Agrp-IRES-Cre 146660999 -1.46 0.10 5.90 0

Arcuate hypothalamic nucleus ARH Erbb4-2A-CreERT2

277854208 -1.22 0.10 5.90 0

Arcuate hypothalamic nucleus ARH Erbb4-2A-CreERT2

306271212 -1.70 0.20 5.90 0

Arcuate hypothalamic nucleus ARH Gal-Cre_KI87 176431817 -1.22 0.10 5.90 0

Arcuate hypothalamic nucleus ARH Gal-Cre_KI87 178282527 -1.70 0.20 5.90 0

Arcuate hypothalamic nucleus ARH Ins2-Cre 286318327 -1.22 0.15 5.45 0

Arcuate hypothalamic nucleus ARH Ins2-Cre 298105299 -1.46 0.10 5.90 0

Arcuate hypothalamic nucleus ARH Kiss1-Cre 232310521 -1.22 0.10 5.90 0

Arcuate hypothalamic nucleus ARH Kiss1-Cre 232311236 -1.70 0.20 5.90 0

Page 11: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 11 of 117

Arcuate hypothalamic nucleus ARH Lepr-IRES-Cre 171482142 -1.46 0.10 5.90 0

Arcuate hypothalamic nucleus ARH Lepr-IRES-Cre 181891892 -1.46 0.10 5.90 0

Arcuate hypothalamic nucleus ARH Pomc-Cre (BL) 175738378 -1.70 0.20 5.90 0

Arcuate hypothalamic nucleus ARH Pomc-Cre (BL) 263369222 -1.22 0.10 5.90 0

Arcuate hypothalamic nucleus ARH Pomc-Cre (ST) 158142090 -1.46 0.10 5.90 0

Arcuate hypothalamic nucleus ARH Pomc-Cre (ST) 159751184 -1.90 0.25 5.40 0

Arcuate hypothalamic nucleus ARH Slc32a1-IRES-Cre

266489212 -1.22 0.10 5.90 0

Arcuate hypothalamic nucleus ARH Tac2-IRES2-Cre 241278553 -1.70 0.20 5.90 0

Arcuate hypothalamic nucleus ARH Th-Cre_FI172 286726777 -1.22 0.10 5.90 0

Auditory areas AUD C57BL/6J 116903230 -2.54 4.20 1.25 0

Auditory areas AUD Rasgrf2-2A-dCre 298719484 -2.46 4.35 0.85 0

Barrington's nucleus B Chat-IRES-Cre 267151656 -5.30 0.80 2.75 0

Basolateral amygdalar nucleus, anterior part

BLAa C57BL/6J 113144533 -1.06 3.00 3.90 0

Basolateral amygdalar nucleus, anterior part

BLAa C57BL/6J 277710753 -0.70 3.00 4.35 0

Basolateral amygdalar nucleus, ventral part

BLAv Slc32a1-IRES-Cre

305321177 -1.70 2.75 5.25 0

Basomedial amygdalar nucleus BMA C57BL/6J 273028004 -1.06 2.75 5.40 0

Basomedial amygdalar nucleus BMA Erbb4-2A-CreERT2

165972951 -0.94 2.60 4.60 0

Basomedial amygdalar nucleus, posterior part

BMAp C57BL/6J 113935990 -1.06 2.50 4.84 0

Basomedial amygdalar nucleus, posterior part

BMAp C57BL/6J 125832322 -1.82 3.25 4.25 10

Page 12: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 12 of 117

Basomedial amygdalar nucleus, posterior part

BMAp Rbp4-Cre_KL100 182294687 -1.70 2.75 5.25 0

Bed nuclei of the stria terminalis BST C57BL/6J 117312486 0.38 0.50 3.90 0

Bed nuclei of the stria terminalis BST C57BL/6J 146747721 0.62 1.20 4.84 0

Bed nuclei of the stria terminalis BST C57BL/6J 147049515 0.02 0.50 3.58 0

Bed nuclei of the stria terminalis BST Cart-Tg1-Cre 176886238 -2.80 0.25 4.90 0

Bed nuclei of the stria terminalis BST Crh-IRES-Cre (ZJH)

204832917 0.38 0.50 3.90 0

Bed nuclei of the stria terminalis BST Erbb4-2A-CreERT2

167026321 0.02 0.50 3.58 0

Bed nuclei of the stria terminalis BST Erbb4-2A-CreERT2

194948535 -0.22 2.75 4.03 30

Bed nuclei of the stria terminalis BST Gad2-IRES-Cre 294005186 0.38 0.70 5.00 0

Bed nuclei of the stria terminalis BST Gad2-IRES-Cre 302016815 0.50 0.90 4.85 0

Bed nuclei of the stria terminalis BST Gad2-IRES-Cre 303537993 0.50 0.50 3.90 0

Bed nuclei of the stria terminalis BST Gpr26-Cre_KO250

305026146 0.26 0.35 4.60 0

Bed nuclei of the stria terminalis BST Htr2a-Cre_KM207

301947600 0.14 1.00 4.07 0

Bed nuclei of the stria terminalis BST Htr3a-Cre_NO152

305645843 0.02 0.50 3.58 0

Bed nuclei of the stria terminalis BST Ppp1r17-Cre_NL146

267763584 -0.10 2.55 4.00 30

Bed nuclei of the stria terminalis BST Ppp1r17-Cre_NL146

267764292 0.38 0.50 3.90 0

Bed nuclei of the stria terminalis BST Rbp4-Cre_KL100 308386222 -0.22 2.75 4.03 30

Bed nuclei of the stria terminalis BST Sim1-Cre 159095796 -0.22 2.75 4.03 30

Bed nuclei of the stria terminalis BST Sim1-Cre 159375036 0.02 0.50 3.58 0

Page 13: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 13 of 117

Bed nuclei of the stria terminalis BST Sim1-Cre 181786681 0.38 0.02 4.20 0

Bed nuclei of the stria terminalis BST Sim1-Cre 241279971 -0.22 2.75 4.03 30

Bed nuclei of the stria terminalis BST Slc17a6-IRES-Cre

167654731 0.10 0.40 3.67 0

Bed nuclei of the stria terminalis BST Slc6a3-Cre 175739085 -0.22 2.75 4.03 30

Bed nuclei of the stria terminalis BST Sst-IRES-Cre 304760810 -0.22 2.75 4.03 30

Bed nuclei of the stria terminalis BST Tac2-IRES2-Cre 265138021 0.14 1.00 4.07 0

Bed nuclei of the stria terminalis, posterior division

BSTpr Htr2a-Cre_KM207

300236763 0.02 0.50 3.58 0

Bed nucleus of the accessory olfactory tract

BA Slc17a6-IRES-Cre

303578324 -1.06 1.70 5.55 0

Bed nucleus of the anterior commissure BAC Cck-IRES-Cre 159433187 0.10 0.40 3.67 0

Caudoputamen CP C57BL/6J 100142580 0.14 1.75 2.53 0

Caudoputamen CP C57BL/6J 112307754 -0.70 2.70 2.39 0

Caudoputamen CP C57BL/6J 112458831 0.14 1.75 2.53 0

Caudoputamen CP C57BL/6J 113505468 0.62 0.29 5.14 -30

Caudoputamen CP C57BL/6J 113766038 -0.70 2.17 1.92 0

Caudoputamen CP C57BL/6J 114399934 0.98 2.65 3.19 0

Caudoputamen CP C57BL/6J 120570964 -1.34 3.00 2.82 0

Caudoputamen CP C57BL/6J 124059700 0.98 0.95 2.12 0

Caudoputamen CP C57BL/6J 127711803 0.62 0.29 5.14 -30

Caudoputamen CP C57BL/6J 127762867 -0.70 2.17 1.92 0

Caudoputamen CP C57BL/6J 146553266 0.98 0.95 2.12 0

Caudoputamen CP C57BL/6J 148198052 0.98 1.90 2.10 0

Page 14: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 14 of 117

Caudoputamen CP C57BL/6J 158916311 0.98 1.90 2.10 0

Caudoputamen CP C57BL/6J 175072215 -0.22 3.25 2.90 0

Caudoputamen CP C57BL/6J 180982124 -0.22 3.25 2.90 0

Caudoputamen CP C57BL/6J 272824561 1.42 2.25 2.85 0

Caudoputamen CP Chat-IRES-Cre 183009881 -1.22 3.05 2.37 0

Caudoputamen CP Chat-IRES-Cre 292959343 0.98 0.95 2.12 0

Caudoputamen CP Cux2-CreERT2 292620968 0.98 2.65 3.19 0

Caudoputamen CP Drd1a-Cre 159223001 0.98 0.95 2.12 0

Caudoputamen CP Drd1a-Cre 159941339 -0.70 2.70 2.39 0

Caudoputamen CP Drd1a-Cre 159942097 -0.70 2.70 3.40 0

Caudoputamen CP Drd1a-Cre 160537018 0.98 1.90 1.95 0

Caudoputamen CP Drd1a-Cre 160537796 0.98 1.05 3.12 0

Caudoputamen CP Drd2-Cre_ER44 127140981 0.14 1.75 2.53 0

Caudoputamen CP Drd2-Cre_ER44 127224133 0.98 0.95 2.12 0

Caudoputamen CP Drd2-Cre_ER44 155736539 -0.70 2.70 3.40 0

Caudoputamen CP Drd2-Cre_ER44 155737254 0.98 0.95 2.12 0

Caudoputamen CP Drd2-Cre_ER44 156670520 -0.70 2.70 2.39 0

Caudoputamen CP Drd2-Cre_ER44 158019342 0.96 1.90 1.95 0

Caudoputamen CP Drd2-Cre_ER44 159329308 0.98 1.05 3.12 0

Caudoputamen CP Drd2-Cre_ER44 160540013 -1.34 2.80 1.84 0

Caudoputamen CP Drd2-Cre_ER44 175732996 -1.34 2.80 1.84 0

Caudoputamen CP Gabrr3-Cre_KC112

161176690 0.38 2.80 2.76 0

Page 15: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 15 of 117

Caudoputamen CP Gad2-IRES-Cre 157911832 -0.70 2.70 2.39 0

Caudoputamen CP Ntrk1-IRES-Cre 265929968 -1.22 3.05 2.37 0

Caudoputamen CP Ntrk1-IRES-Cre 287994474 -1.34 2.80 1.84 0

Caudoputamen CP Ntrk1-IRES-Cre 287995180 -0.70 2.70 2.39 0

Caudoputamen CP Ntrk1-IRES-Cre 310175667 0.98 0.95 2.12 0

Caudoputamen CP Pcdh9-Cre 286311648 -1.34 2.80 1.84 0

Caudoputamen CP Penk-2A-CreERT2

278434443 0.14 1.75 2.53 0

Caudoputamen CP Plxnd1-Cre 293366035 -1.34 2.80 1.84 0

Caudoputamen CP Plxnd1-Cre 293366741 -0.70 2.17 1.92 0

Caudoputamen CP Ppp1r17-Cre_NL146

286649703 -2.18 3.25 3.60 0

Caudoputamen CP Slc32a1-IRES-Cre

264095536 -2.92 1.75 3.45 0

Caudoputamen CP Th-Cre_FI172 272697238 -1.22 3.05 2.37 0

Central amygdalar nucleus CEA C57BL/6J 112459547 -1.22 2.77 3.80 0

Central amygdalar nucleus CEA C57BL/6J 117317884 -1.46 3.55 3.70 0

Central amygdalar nucleus CEA C57BL/6J 120282354 -1.46 3.55 3.70 0

Central amygdalar nucleus CEA C57BL/6J 146795148 -0.58 1.75 4.50 0

Central amygdalar nucleus CEA C57BL/6J 175072921 -0.70 2.20 5.00 0

Central amygdalar nucleus CEA Crh-IRES-Cre (ZJH)

267152406 -0.94 2.25 4.47 0

Central amygdalar nucleus CEA Erbb4-2A-CreERT2

120281646 -0.94 2.43 4.47 0

Central amygdalar nucleus CEA Erbb4-2A-CreERT2

120435569 -1.22 2.77 3.80 0

Page 16: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 16 of 117

Central amygdalar nucleus CEA Etv1-CreERT2 181889764 -1.06 2.70 3.90 0

Central amygdalar nucleus CEA Etv1-CreERT2 181890477 -1.22 2.34 4.75 0

Central amygdalar nucleus CEA Etv1-CreERT2 286774064 -1.06 2.70 3.90 0

Central amygdalar nucleus CEA Prkcd-GluCla-CFP-IRES-Cre

265945645 -1.82 2.65 4.25 0

Central amygdalar nucleus CEA Slc18a2-Cre_OZ14

265648940 -0.94 2.25 4.47 0

Central amygdalar nucleus CEA Tac2-IRES2-Cre 241279261 -0.94 2.25 4.47 0

Central amygdalar nucleus, capsular part

CEAc C57BL/6J 127761449 -1.06 2.50 4.84 0

Central lateral nucleus of the thalamus CL Crh-IRES-Cre (BL)

182805965 -0.58 1.00 2.93 0

Central lateral nucleus of the thalamus CL Gal-Cre_KI87 175817683 -1.58 0.68 2.73 0

Central lateral nucleus of the thalamus CL Grm2-Cre_MR90 175740500 -1.58 0.68 2.73 0

Central lateral nucleus of the thalamus CL Rbp4-Cre_KL100 183174303 -2.06 1.25 2.97 0

Central linear nucleus raphe CLI Calb2-IRES-Cre 301765327 -4.16 0.25 5.65 0

Central linear nucleus raphe CLI Syt17-Cre_NO14 127651139 -3.28 0.36 4.13 0

Central medial nucleus of the thalamus CM C57BL/6J 147135107 -1.06 0.20 3.40 0

Central medial nucleus of the thalamus CM C57BL/6J 147787606 -1.34 0.32 4.05 0

Central medial nucleus of the thalamus CM C57BL/6J 158841171 -1.46 0.13 4.00 0

Central medial nucleus of the thalamus CM C57BL/6J 273025166 -1.22 0.13 4.00 0

Central medial nucleus of the thalamus CM Calb2-IRES-Cre 182888003 -1.06 0.20 3.40 0

Central medial nucleus of the thalamus CM Gal-Cre_KI87 168004394 -1.06 0.20 3.40 0

Central medial nucleus of the thalamus CM Grm2-Cre_MR90 284665639 -1.06 0.20 3.40 0

Central medial nucleus of the thalamus CM Grp-Cre_KH288 183057424 -1.06 0.20 3.40 0

Page 17: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 17 of 117

Central medial nucleus of the thalamus CM Grp-Cre_KH288 301324895 -1.06 0.20 3.40 0

Central medial nucleus of the thalamus CM Lypd6-Cre_KL156

298050269 -1.06 0.20 3.40 0

Central medial nucleus of the thalamus CM Lypd6-Cre_KL156

303710632 -1.46 0.13 1.45 0

Central medial nucleus of the thalamus CM Plxnd1-Cre 293367448 -1.34 0.50 3.40 0

Central medial nucleus of the thalamus CM Plxnd1-Cre 301538025 -1.06 0.20 3.40 0

Claustrum CLA A930038C07Rik-Tg1-Cre

292375491 1.10 3.25, 3.00 1.90, 2.35

0

Claustrum CLA C57BL/6J 180436360 -0.34 4.00 2.60 0

Claustrum CLA Cux2-IRES-Cre 293473098 -0.34 3.85 3.00 0

Claustrum CLA Cux2-IRES-Cre 296047806 1.78 2.40, 2.80 2.24 0

Claustrum CLA Oxtr-Cre_ON66 278171908 1.70 1.85 2.83 0

Claustrum CLA Oxtr-Cre_ON66 292372636 -1.46 3.75 3.40 0

Copula pyramidis COPY Prkcd-GluCla-CFP-IRES-Cre

267611175 -6.12 2.25 2.90 0

Cortical amygdalar area, posterior part, lateral zone

COApl C57BL/6J 115958115 -1.22 2.34 4.75 0

Cortical amygdalar area, posterior part, lateral zone

COApl C57BL/6J 122641078 -0.58 2.75 5.40 0

Cortical amygdalar area, posterior part, lateral zone

COApl C57BL/6J 129573239 -1.70 2.75 5.25 0

Cortical amygdalar area, posterior part, lateral zone

COApl C57BL/6J 277480964 -2.30 2.75 4.70 0

Cortical amygdalar area, posterior part, lateral zone

COApl Gad2-IRES-Cre 305124396 -0.46 2.20 5.22 0

Cortical amygdalar area, posterior part, lateral zone

COApl Grik4-Cre 168302154 -1.70 2.75 5.25 0

Page 18: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 18 of 117

Cortical amygdalar area, posterior part, lateral zone

COApl Rbp4-Cre_KL100 304721447 -1.34 1.75 4.50 0

Cortical amygdalar area, posterior part, lateral zone

COApl Slc17a6-IRES-Cre

266962653 -1.70 2.75 5.25 0

Cortical amygdalar area, posterior part, lateral zone

COApl Slc17a7-IRES2-Cre

267150949 -1.70 2.75 5.25 0

Cortical amygdalar area, posterior part, medial zone

COApm C57BL/6J 114249084 -2.70 2.80 5.07 0

Cortical amygdalar area, posterior part, medial zone

COApm C57BL/6J 125802444 -2.46 2.75 4.75 0

Cortical amygdalar area, posterior part, medial zone

COApm Sim1-Cre 170946889 -1.58 1.80 5.45 0

Cortical amygdalar area, posterior part, medial zone

COApm Slc32a1-IRES-Cre

299623085 -2.46 2.75 4.75 0

Crus 1 ANcr1 C57BL/6J 112827872 -6.48 3.00 0.98 0

Crus 1 ANcr1 Gabra6-IRES-Cre

181116850 -6.48 2.50 0.57 0

Crus 1 ANcr1 Grm2-Cre_MR90 287879384 -6.48 2.50 0.57 0

Crus 1 ANcr1 Grm2-Cre_MR90 301324157 -6.48 2.50 0.57 0

Crus 1 ANcr1 Pcp2-Cre_GN135

147633169 -6.48 2.50 0.57 0

Crus 1 ANcr1 Pvalb-IRES-Cre 167201465 -6.48 2.50 0.57 0

Crus 2 ANcr2 C57BL/6J 142654808 -6.48 2.50 0.57 0

Crus 2 ANcr2 Pcp2-Cre_GN135

168230532 -6.48 3.00 0.98 0

Cuneiform nucleus CUN C57BL/6J 120571672 -5.02 1.20 2.30 0

Cuneiform nucleus CUN C57BL/6J 126522350 -4.48 1.15 2.80 0

Dentate gyrus DG A930038C07Rik-Tg1-Cre

298232793 1.70 0.40 2.00 0

Page 19: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 19 of 117

Dentate gyrus DG Adcyap1-2A-Cre 287247261 -3.52 2.50 3.50 0

Dentate gyrus DG C57BL/6J 100141214 -1.70 0.70 2.04 0

Dentate gyrus DG C57BL/6J 100148143 -1.70 0.70 2.04 0

Dentate gyrus DG C57BL/6J 112167395 interaural 0.00

1.50 1.77 0

Dentate gyrus DG C57BL/6J 112672268 -4.04 3.25 2.60 0

Dentate gyrus DG C57BL/6J 112745787 -2.30 1.75 1.66 0

Dentate gyrus DG C57BL/6J 113166056 -3.52 2.50 3.50 0

Dentate gyrus DG C57BL/6J 114008220 -2.92 1.85 1.95 0

Dentate gyrus DG C57BL/6J 114430043 -3.52 2.75 2.34 0

Dentate gyrus DG C57BL/6J 272970039 -0.80 0.25 2.45 0

Dentate gyrus DG Drd3-Cre_KI198 301122593 -1.70 0.70 2.04 0

Dentate gyrus DG Gad2-IRES-Cre 305400137 -1.70 0.70 2.04 0

Dentate gyrus DG Gal-Cre_KI87 266173339 -3.52 2.75 2.34 0

Dentate gyrus DG Grik4-Cre 113933871 -2.30 1.75 1.66 0

Dentate gyrus DG Grik4-Cre 114009636 -1.70 0.70 2.04 0

Dentate gyrus DG Grik4-Cre 114047146 -2.92 1.85 1.95 0

Dentate gyrus DG Grik4-Cre 182029174 -3.52 2.50 3.50 0

Dentate gyrus DG Grm2-Cre_MR90 264709761 -2.30 1.75 1.66 0

Dentate gyrus DG Grm2-Cre_MR90 264872385 -3.52 2.75 2.34 0

Dentate gyrus DG Grm2-Cre_MR90 287097454 -1.70 0.70 2.04 0

Dentate gyrus DG Grm2-Cre_MR90 287171983 -2.92 1.85 1.95 0

Dentate gyrus DG Lypd6-Cre_KL156

299857813 -1.70 0.70 2.04 0

Page 20: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 20 of 117

Dentate gyrus DG Nos1-CreERT2 301327022 -1.70 0.70 2.04 0

Dentate gyrus DG Oxtr-Cre_ON66 301422682 -1.70 0.70 2.04 0

Dentate gyrus DG Pomc-Cre (BL) 159996191 -1.70 0.70 2.04 0

Dentate gyrus DG Pomc-Cre (BL) 160079360 -3.52 2.75 2.34 0

Dentate gyrus DG Pomc-Cre (ST) 113780276 -2.30 1.75 1.66 0

Dentate gyrus DG Ppp1r17-Cre_NL146

278504263 -1.34 0.75 2.24 0

Dentate gyrus DG Ppp1r17-Cre_NL146

308550233 -1.70 0.70 2.04 0

Dentate gyrus DG Rbp4-Cre_KL100 182295393 -1.70 0.70 2.04 0

Dentate gyrus DG Rbp4-Cre_KL100 183376982 -2.92 1.85 1.95 0

Dentate gyrus DG Rbp4-Cre_KL100 266250904 -2.30 1.75 1.66 0

Dentate gyrus DG Rbp4-Cre_KL100 266409949 -3.52 2.75 2.34 0

Dentate gyrus DG Slc17a7-IRES2-Cre

293788700 -3.16 2.10 2.85 0

Dentate gyrus DG Slc17a7-IRES2-Cre

293787994 -2.18 1.45 2.44 0

Dentate gyrus DG Slc32a1-IRES-Cre

305320171 -1.70 0.70 2.04 0

Dentate gyrus DG Syt17-Cre_NO14 288322797 -1.70 0.70 2.04 0

Dentate gyrus DG Syt17-Cre_NO14 293011049 -2.30 1.75 1.66 0

Dentate gyrus DG Syt17-Cre_NO14 293011759 -3.52 2.75 2.34 0

Dentate gyrus DG Syt17-Cre_NO14 293115527 -1.34 0.75 2.24 0

Dentate nucleus DN C57BL/6J 268389532 -6.24 2.20 2.25 0

Dentate nucleus DN Gad2-IRES-Cre 304675254 -6.12 2.25 2.90 0

Page 21: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 21 of 117

Dentate nucleus DN Slc17a6-IRES-Cre

286608092 -5.88 2.25 2.19 0

Diagonal band nucleus NDB Chat-IRES-Cre 167200755 0.50 0.81 4.84 0

Diagonal band nucleus NDB Chat-IRES-Cre 177605425 0.98 0.25 4.60 0

Diagonal band nucleus NDB Ntrk1-IRES-Cre 286319739 0.62 1.20 4.85 0

Dorsal auditory area AUDd C57BL/6J 115958825 -3.08 4.00 0.80 0

Dorsal auditory area AUDd C57BL/6J 139519496 -2.46 4.25 0.81 0

Dorsal auditory area AUDd C57BL/6J 146858006 -3.08 4.00 0.80 0

Dorsal auditory area AUDd C57BL/6J 158314278 -2.46 4.00 0.65 0

Dorsal auditory area AUDd C57BL/6J 180073473 -3.40 4.00 1.07 0

Dorsal auditory area AUDd Cux2-IRES-Cre 176430283 -2.46 4.25 0.81 0

Dorsal auditory area AUDd Erbb4-2A-CreERT2

156743264 -2.46 4.25 0.81 0

Dorsal auditory area AUDd Nr5a1-Cre 114752488 -2.46 4.25 0.81 0

Dorsal auditory area AUDd Ntsr1-Cre_GN220

120494024 -2.46 4.25 0.81 0

Dorsal auditory area AUDd Pvalb-IRES-Cre 160080068 -2.46 4.25 0.81 0

Dorsal auditory area AUDd Tac1-IRES2-Cre 181372049 -2.46 4.25 0.81 0

Dorsal auditory area AUDd Tac2-IRES2-Cre 268075711 -2.46 4.35 0.90 0

Dorsal cochlear nucleus DCO C57BL/6J 143515102 -5.52 1.16 3.70 -20

Dorsal cochlear nucleus DCO C57BL/6J 146794439 -5.20 1.95 3.50 0

Dorsal cochlear nucleus DCO Crh-IRES-Cre (BL)

167213641 -6.12 2.25 2.80 0

Dorsal cochlear nucleus DCO Crh-IRES-Cre (BL)

266839784 -6.12 2.25 2.90 0

Dorsal cochlear nucleus DCO Gad2-IRES-Cre 287664997 -6.12 2.25 2.90 0

Page 22: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 22 of 117

Dorsal cochlear nucleus DCO Pnmt-Cre 177903648 -6.12 2.25 2.80 0

Dorsal cochlear nucleus DCO Prkcd-GluCla-CFP-IRES-Cre

292319155 -6.12 2.25 2.90 0

Dorsal cochlear nucleus DCO Slc17a6-IRES-Cre

286556914 -6.12 2.25 2.90 0

Dorsal cochlear nucleus DCO Slc6a5-Cre_KF109

160152987 -6.12 2.25 2.80 0

Dorsal motor nucleus of the vagus nerve

DMX Chat-IRES-Cre 264564375 0.00 calamus

(-7.32 bregma)

0.25 0.48 0

Dorsal motor nucleus of the vagus nerve

DMX Gad2-IRES-Cre 303536573 0 calamus

0.25 0.48 0

Dorsal motor nucleus of the vagus nerve

DMX Nxph4-2A-CreERT2

304612686 0 calamus

0.05 0.20 0

Dorsal motor nucleus of the vagus nerve

DMX Ppp1r17-Cre_NL146

268323342 0.00 calamus

(-7.32 bregma)

0.25 0.48 0

Dorsal motor nucleus of the vagus nerve

DMX Slc18a2-Cre_OZ14

287096578 0.00 calamus

(-7.32 bregma)

0.25 0.48 0

Dorsal motor nucleus of the vagus nerve

DMX Slc6a3-Cre 171021122 0.00 calamus

(-7.32 bregma)

0.25 0.48 0

Dorsal motor nucleus of the vagus nerve

DMX Syt17-Cre_NO14 263784128 0.00 calamus

(-7.32 bregma)

0.25 0.48 0

Dorsal nucleus raphe DR C57BL/6J 114155923 -4.24 0.52 2.86 10

Dorsal nucleus raphe DR Drd3-Cre_KI196 300111793 -3.80 0.04 2.85 0

Page 23: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 23 of 117

Dorsal nucleus raphe DR Slc6a4-Cre_ET33

128055110 -4.24 0.52 2.86 10

Dorsal nucleus raphe DR Slc6a4-Cre_ET33

129564675 -4.36 0.18 2.10 0

Dorsal nucleus raphe DR Slc6a4-Cre_ET33

168300027 -3.88 0.20 3.30 0

Dorsal nucleus raphe DR Slc6a4-CreERT2_EZ13

114155190 -4.24 0.52 2.86 10

Dorsal nucleus raphe DR Slc6a4-CreERT2_EZ13

114248377 -4.36 0.18 2.10 0

Dorsal nucleus raphe DR Th-Cre_FI172 266500714 -4.24 0.52 2.86 10

Dorsal part of the lateral geniculate complex

LGd C57BL/6J 100141598 -2.30 2.00 2.44 0

Dorsal part of the lateral geniculate complex

LGd Gal-Cre_KI87 266248776 -2.30 2.00 2.60 0

Dorsal part of the lateral geniculate complex

LGd Htr2a-Cre_KM207

298004028 -2.00 2.15 2.60 0

Dorsal part of the lateral geniculate complex

LGd Htr2a-Cre_KM207

298003295 -2.30 2.00 2.60 0

Dorsal part of the lateral geniculate complex

LGd Prkcd-GluCla-CFP-IRES-Cre

292320572 -2.00 2.15 2.60 0

Dorsal part of the lateral geniculate complex

LGd Scnn1a-Tg2-Cre 156198187 -2.30 2.00 2.44 0

Dorsal part of the lateral geniculate complex

LGd Scnn1a-Tg2-Cre 263241470 -2.30 2.00 2.60 0

Dorsal part of the lateral geniculate complex

LGd Slc17a6-IRES-Cre

293914056 -2.30 2.00 2.60 0

Dorsal part of the lateral geniculate complex

LGd Slc17a6-IRES-Cre

293914766 -2.00 2.15 2.60 0

Dorsal part of the lateral geniculate complex

LGd Slc17a7-IRES2-Cre

293787288 -2.30 2.00 2.60 0

Page 24: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 24 of 117

Dorsal part of the lateral geniculate complex

LGd Slc18a2-Cre_OZ14

287458189 -2.00 2.15 2.60 0

Dorsal part of the lateral geniculate complex

LGd Slc18a2-Cre_OZ14

287458895 -2.30 2.00 2.60 0

Dorsal part of the lateral geniculate complex

LGd Slc18a2-Cre_OZ14

301735795 -2.30 2.00 2.60 0

Dorsal peduncular area DP C57BL/6J 112597496 1.70 0.25 2.47 0

Dorsal premammillary nucleus PMd C57BL/6J 146659588 -1.46 0.39 5.50 0

Dorsal premammillary nucleus PMd Tac1-IRES2-Cre 294316542 -2.70 0.13 5.20 0

Dorsomedial nucleus of the hypothalamus

DMH C57BL/6J 175106053 -0.58 0.20 4.75 0

Dorsomedial nucleus of the hypothalamus

DMH Cart-Tg1-Cre 298833739 -1.46 0.39 5.50 0

Dorsomedial nucleus of the hypothalamus

DMH Gad2-IRES-Cre 287538943 -1.50 0.35 5.30 0

Dorsomedial nucleus of the hypothalamus

DMH Gal-Cre_KI87 178283239 -1.50 0.35 5.20 0

Dorsomedial nucleus of the hypothalamus

DMH Gal-Cre_KI87 266248065 -1.50 0.35 5.20 0

Dorsomedial nucleus of the hypothalamus

DMH Hdc-Cre_IM1 168616827 -1.70 0.35 4.90 0

Dorsomedial nucleus of the hypothalamus

DMH Ins2-Cre 265813096 -1.22 0.94 5.04 10

Dorsomedial nucleus of the hypothalamus

DMH Lepr-IRES-Cre 113314337 -1.46 0.39 5.30 0

Dorsomedial nucleus of the hypothalamus

DMH Lepr-IRES-Cre 160317628 -1.70 0.36 4.89 0

Dorsomedial nucleus of the hypothalamus

DMH Nr5a1-Cre 182336846 -1.46 0.39 5.30 0

Dorsomedial nucleus of the hypothalamus

DMH Ppp1r17-Cre_NL146

308641549 -1.50 0.35 5.30 0

Page 25: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 25 of 117

Dorsomedial nucleus of the hypothalamus

DMH Rasgrf2-2A-dCre 313325371 -1.46 0.39 5.50 0

Dorsomedial nucleus of the hypothalamus

DMH Sim1-Cre 159222295 -0.94 0.25 4.52 0

Dorsomedial nucleus of the hypothalamus

DMH Sim1-Cre_KJ18 266837456 -1.46 0.39 5.50 0

Ectorhinal area ECT A930038C07Rik-Tg1-Cre

264630726 -4.36 4.25 1.40 0

Ectorhinal area ECT A930038C07Rik-Tg1-Cre

286837316 -4.04 3.80 1.90 0

Ectorhinal area ECT C57BL/6J 180403712 -2.00 4.20 2.15 0

Ectorhinal area ECT C57BL/6J 272414403 -4.36 4.25 1.40 0

Ectorhinal area ECT Cux2-IRES-Cre 278317239 -4.04 3.80 1.90 0

Ectorhinal area ECT Gpr26-Cre_KO250

301264977 -4.36 4.00 1.25 0

Ectorhinal area ECT Gpr26-Cre_KO250

301265683 -4.36 4.25 1.35 0

Ectorhinal area ECT Rbp4-Cre_KL100 182794184 -4.36 4.25 1.40 0

Endopiriform nucleus, dorsal part EPd C57BL/6J 158321996 -0.22 3.70 3.25 0

Endopiriform nucleus, dorsal part EPd Gad2-IRES-Cre 305403845 -1.46 4.00 3.70 0

Endopiriform nucleus, dorsal part EPd Htr2a-Cre_KM207

308549214 -1.46 3.75 3.40 0

Endopiriform nucleus, dorsal part EPd Kcnc2-Cre 126853068 0.98 2.85 3.14 0

Endopiriform nucleus, dorsal part EPd Kcnc2-Cre 126863090 -1.46 3.75 3.40 0

Endopiriform nucleus, dorsal part EPd Oxtr-Cre_ON66 267762146 0.98 2.65 3.19 0

Endopiriform nucleus, dorsal part EPd Oxtr-Cre_ON66 267762859 0.98 2.85 3.14 0

Endopiriform nucleus, dorsal part EPd Syt17-Cre_NO14 187268452 0.98 3.00 3.14 0

Page 26: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 26 of 117

Endopiriform nucleus, ventral part EPv Efr3a-Cre_NO108

299244730 -0.94 2.60 4.60 0

Entorhinal area ENT Grm2-Cre_MR90 267747690 -4.21 3.40 2.20, 2.60

0

Entorhinal area ENT Scnn1a-Tg2-Cre 268041795 -4.59 3.40 2.20, 2.60

0

Entorhinal area ENT Scnn1a-Tg3-Cre 287770700 -4.43 3.40 2.20, 2.60

0

Entorhinal area ENT Sst-IRES-Cre 288321385 -4.72 3.40 2.20, 2.60

0

Entorhinal area ENT Syt17-Cre_NO14 288322091 -4.16 3.80 3.00 0

Entorhinal area, lateral part ENTl A930038C07Rik-Tg1-Cre

298798846 -3.16 4.25 2.76 0

Entorhinal area, lateral part ENTl A930038C07Rik-Tg1-Cre

298797996 -4.16 3.80 3.00 0

Entorhinal area, lateral part ENTl C57BL/6J 114472145 -3.16 4.25 2.76 0

Entorhinal area, lateral part ENTl C57BL/6J 126116848 -3.40 4.10 3.05 0

Entorhinal area, lateral part ENTl C57BL/6J 127397469 -2.70 4.25 2.75 0

Entorhinal area, lateral part ENTl C57BL/6J 142654100 -4.36 4.00 1.25 0

Entorhinal area, lateral part ENTl C57BL/6J 146553971 1.18 0.70 4.15 0

Entorhinal area, lateral part ENTl C57BL/6J 180297139 -4.36 3.90 1.40 0

Entorhinal area, lateral part ENTl Chrna2-Cre_OE25

299857096 -4.16 3.80 3.00 0

Entorhinal area, lateral part ENTl Cux2-CreERT2 181859467 -4.72 3.37 2.11, 2.60

0

Entorhinal area, lateral part ENTl Cux2-IRES-Cre 263974698 -4.36 4.25 1.40 0

Entorhinal area, lateral part ENTl Cux2-IRES-Cre 272779830 -4.36 4.25 1.30 0

Entorhinal area, lateral part ENTl Cux2-IRES-Cre 287953223 -4.22 3.40 2.20 0

Page 27: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 27 of 117

Entorhinal area, lateral part ENTl Cux2-IRES-Cre 287952517 -3.16 4.25 2.76 0

Entorhinal area, lateral part ENTl Drd3-Cre_KI196 293702482 -3.16 4.25 2.76 0

Entorhinal area, lateral part ENTl Grm2-Cre_MR90 183225124 -3.16 4.25 2.76 0

Entorhinal area, lateral part ENTl Htr2a-Cre_KM207

301988879 -3.16 4.25 2.76 0

Entorhinal area, lateral part ENTl Ntsr1-Cre_GN220

159602279 -4.24 4.00 1.65 0

Entorhinal area, lateral part ENTl Otof-Cre 167212932 -3.40 4.10 3.05 0

Entorhinal area, lateral part ENTl Otof-Cre 181891184 -4.16 3.80 3.00 0

Entorhinal area, lateral part ENTl Otof-Cre 182226133 -3.16 4.25 2.76 0

Entorhinal area, lateral part ENTl Pcdh9-Cre 267211671 -4.60 3.75 1.55 0

Entorhinal area, lateral part ENTl Penk-IRES2-Cre 305973112 -4.16 3.80 3.00 0

Entorhinal area, lateral part ENTl Plxnd1-Cre 301464114 -2.70 2.80 5.07 0

Entorhinal area, lateral part ENTl Rbp4-Cre_KL100 232311959 -4.24 4.00 1.65 0

Entorhinal area, lateral part ENTl Rbp4-Cre_KL100 286483411 -3.16 4.25 2.76 0

Entorhinal area, lateral part ENTl Scnn1a-Tg3-Cre 287769992 -4.04 3.80 1.90 0

Entorhinal area, lateral part ENTl Syt17-Cre_NO14 293009265 -3.16 4.25 2.76 0

Entorhinal area, lateral part ENTl Wfs1-Tg2-CreERT2

278435864 -4.32 3.40 2.20, 2.60

0

Entorhinal area, lateral part ENTl Wfs1-Tg2-CreERT2

278435152 -4.35 3.40 2.20, 2.60

0

Entorhinal area, lateral part ENTl Wfs1-Tg3-CreERT2

182516286 -3.16 4.25 2.76 0

Entorhinal area, medial part, dorsal zone

ENTm C57BL/6J 112672974 -4.72 3.37 2.11, 2.60

0

Entorhinal area, medial part, dorsal zone

ENTm C57BL/6J 113226232 -4.16 3.80 3.00 0

Page 28: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 28 of 117

Entorhinal area, medial part, dorsal zone

ENTm C57BL/6J 127139568 -4.48 3.00 3.44 0

Entorhinal area, medial part, dorsal zone

ENTm Calb1-2A-dgCre 293750063 -4.72 3.40 2.20, 2.60

0

Entorhinal area, medial part, dorsal zone

ENTm Cux2-CreERT2 194947823 -4.96 3.10 2.65 0

Entorhinal area, medial part, dorsal zone

ENTm Cux2-CreERT2 264873092 -4.45 3.40 2.60 0

Entorhinal area, medial part, dorsal zone

ENTm Cux2-CreERT2 264873809 -4.58 3.40 2.60 0

Entorhinal area, medial part, dorsal zone

ENTm Drd3-Cre_KI196 300078194 -4.72 3.40 2.2, 2.6

0

Entorhinal area, medial part, dorsal zone

ENTm Grik4-Cre 267998328 -4.04 3.40 2.20, 2.60

0

Entorhinal area, medial part, dorsal zone

ENTm Grik4-Cre 267999034 -4.23 3.40 2.20, 2.60

0

Entorhinal area, medial part, dorsal zone

ENTm Htr2a-Cre_KM207

300319630 -4.16 3.80 3.00 0

Entorhinal area, medial part, dorsal zone

ENTm Nos1-CreERT2 299403823 -4.40 3.40 2.2, 2.6

0

Entorhinal area, medial part, dorsal zone

ENTm Pcdh9-Cre 308642254 -4.72 3.40 2.20 0

Entorhinal area, medial part, dorsal zone

ENTm Pcdh9-Cre_NP276

308721177 -4.60 2.40 2.95 0

Entorhinal area, medial part, dorsal zone

ENTm Scnn1a-Tg2-Cre 299447153 -4.34 3.40 2.60 0

Entorhinal area, medial part, dorsal zone

ENTm Scnn1a-Tg2-Cre 302014692 -4.47 3.40 2.65 0

Entorhinal area, medial part, dorsal zone

ENTm Syt17-Cre_NO14 286484879 -4.72 3.40 2.20, 2.60

0

Entorhinal area, medial part, dorsal zone

ENTm Wfs1-Tg3-CreERT2

167793416 -4.16 3.80 3.00 0

Page 29: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 29 of 117

Facial motor nucleus VII C57BL/6J 123663689 -5.34 1.11 4.80 0

Facial motor nucleus VII C57BL/6J 147214398 -5.02 1.11 4.80 0

Facial motor nucleus VII Chat-IRES-Cre 157712456 -6.00 1.15 4.57 0

Facial motor nucleus VII Chat-IRES-Cre 301800314 -4.16 1.00 5.70 0

Facial motor nucleus VII Grik4-Cre 113766744 -6.00 1.15 4.57 0

Facial motor nucleus VII Scnn1a-Tg2-Cre 177905562 -6.00 1.15 4.57 0

Fastigial nucleus FN C57BL/6J 127650431 -6.36 0.75 2.40 0

Field CA1 CA1 C57BL/6J 100147861 -1.70 1.60 1.17 0

Field CA1 CA1 C57BL/6J 100148443 -3.52 3.50 2.07 0

Field CA1 CA1 C57BL/6J 116900714 -2.30 1.25 1.25 0

Field CA1 CA1 C57BL/6J 120436274 -2.30 1.25 1.25 0

Field CA1 CA1 C57BL/6J 120494729 -2.46 2.50 1.34 0

Field CA1 CA1 Chrna2-Cre_OE25

297894255 -4.04 3.80 1.90 0

Field CA1 CA1 Cux2-IRES-Cre 294397907 -4.04 3.80 1.90 0

Field CA1 CA1 Drd3-Cre_KI198 301119459 -2.46 2.50 1.34 0

Field CA1 CA1 Drd3-Cre_KI198 301130077 -1.70 1.60 1.17 0

Field CA1 CA1 Etv1-CreERT2 171019004 -1.70 1.60 1.17 0

Field CA1 CA1 Etv1-CreERT2 175718634 -2.92 3.00 3.45 0

Field CA1 CA1 Etv1-CreERT2 181093729 -3.52 3.50 2.07 0

Field CA1 CA1 Gad2-IRES-Cre 305380411 -2.46 2.50 1.34 0

Field CA1 CA1 Gpr26-Cre_KO250

286554017 -2.46 2.50 1.34 0

Field CA1 CA1 Kcnc2-Cre 182843806 -2.46 2.50 1.34 0

Page 30: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 30 of 117

Field CA1 CA1 Nos1-CreERT2 301325601 -2.46 2.50 1.34 0

Field CA1 CA1 Ppp1r17-Cre_NL146

278503555 -1.70 0.70 2.04 0

Field CA1 CA1 Ppp1r17-Cre_NL146

292479421 -1.70 0.50 1.70 0

Field CA1 CA1 Ppp1r17-Cre_NL146

292532771 -2.92 1.17 1.40 0

Field CA1 CA1 Ppp1r17-Cre_NL146

292532065 -3.52 2.50 1.35 0

Field CA1 CA1 Sim1-Cre 181777177 -1.70 0.50 1.70 0

Field CA1 CA1 Slc17a7-IRES2-Cre

267104205 -2.46 2.50 1.34 0

Field CA1 CA1 Slc17a7-IRES2-Cre

286317619 -1.70 0.70 2.04 0

Field CA1 CA1 Slc32a1-IRES-Cre

305381127 -2.46 2.50 1.34 0

Field CA1 CA1 Syt17-Cre_NO14 286610923 -3.52 3.50 2.07 0

Field CA1 CA1 Vipr2-Cre_KE2 180405830 -2.46 2.50 1.34 0

Field CA1 CA1 Vipr2-Cre_KE2 180520968 -2.30 1.25 1.25 0

Field CA1 CA1 Vipr2-Cre_KE2 182226839 -3.52 3.50 2.07 0

Field CA3 CA3 C57BL/6J 112308468 -2.46 2.60 2.36 0

Field CA3 CA3 C57BL/6J 112745073 -1.70 2.00 1.85 0

Field CA3 CA3 C57BL/6J 113935285 -2.80 2.85 3.00 0

Field CA3 CA3 C57BL/6J 114429338 -2.30 2.97 1.80 0

Field CA3 CA3 C57BL/6J 127649005 -2.92 3.00 3.45 0

Field CA3 CA3 C57BL/6J 180523704 -1.82 2.05 2.42 0

Field CA3 CA3 C57BL/6J 272404772 -2.30 2.75 1.75 0

Page 31: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 31 of 117

Field CA3 CA3 Drd3-Cre_KI198 301120618 -2.46 2.60 2.25 0

Field CA3 CA3 Gad2-IRES-Cre 266488504 -2.54 4.25 3.32 25

Field CA3 CA3 Grik4-Cre 177606858 -2.46 2.60 2.36 0

Field CA3 CA3 Grik4-Cre 177780284 -1.70 2.00 1.85 0

Field CA3 CA3 Grik4-Cre 178382220 -2.80 2.85 3.00 0

Field CA3 CA3 Grik4-Cre 179643824 -2.30 2.97 1.80 0

Field CA3 CA3 Grp-Cre_KH288 179644545 -2.46 2.60 2.36 0

Field CA3 CA3 Grp-Cre_KH288 179902073 -1.70 2.00 1.85 0

Field CA3 CA3 Grp-Cre_KH288 182615063 -2.30 2.97 1.80 0

Field CA3 CA3 Grp-Cre_KH288 182615771 -2.80 2.85 3.00 0

Field CA3 CA3 Kcnc2-Cre 182933935 -2.46 2.60 2.36 0

Field CA3 CA3 Nos1-CreERT2 301326316 -2.46 2.60 2.25 0

Field CA3 CA3 Oxtr-Cre_ON66 301421960 -2.46 2.60 2.25 0

Field CA3 CA3 Ppp1r17-Cre_NL146

278318653 -2.46 2.60 2.36 0

Field CA3 CA3 Ppp1r17-Cre_NL146

278319402 -1.70 2.00 1.85 0

Field CA3 CA3 Ppp1r17-Cre_NL146

278398243 -2.30 2.97 1.80 0

Field CA3 CA3 Ppp1r17-Cre_NL146

278399657 -3.52 2.50 3.50 0

Field CA3 CA3 Prkcd-GluCla-CFP-IRES-Cre

171274191 -1.70 2.00 1.85 0

Field CA3 CA3 Syt17-Cre_NO14 249402769 -3.08 3.00 3.60 0

Flocculus FL C57BL/6J 112789899 -4.24 2.36 3.58 0

Flocculus FL Nos1-CreERT2 304997333 -5.20 1.25 2.80 0

Page 32: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 32 of 117

Gigantocellular reticular nucleus GRN A930038C07Rik-Tg1-Cre

299995638 0.0 calamus

0.05 1.00 0

Gigantocellular reticular nucleus GRN C57BL/6J 125437921 -6.12 0.35 4.90 0

Gigantocellular reticular nucleus GRN C57BL/6J 126188607 -6.24 0.85 4.40 0

Gigantocellular reticular nucleus GRN C57BL/6J 126710034 -6.48 1.00 4.82 0

Gigantocellular reticular nucleus GRN C57BL/6J 126843905 -6.72 0.50 4.55 0

Gigantocellular reticular nucleus GRN C57BL/6J 127041832 -0.24 calamus

(-7.56 bregma)

0.50 1.75 0

Gigantocellular reticular nucleus GRN C57BL/6J 147706228 -5.02 0.50 5.25 0

Gigantocellular reticular nucleus GRN Dbh-Cre_KH212 287029894 -5.68 0.80 5.20 0

Gigantocellular reticular nucleus GRN Gad2-IRES-Cre 287876212 -6.12 0.35 4.90 0

Gigantocellular reticular nucleus GRN Pdzk1ip1-Cre_KD31

182030590 -5.34 1.11 4.80 0

Gigantocellular reticular nucleus GRN Slc17a6-IRES-Cre

286609510 -6.12 0.35 4.90 0

Gigantocellular reticular nucleus GRN Slc32a1-IRES-Cre

303468314 -5.88 2.25 5.30 25

Gigantocellular reticular nucleus GRN Slc32a1-IRES-Cre

305293928 -6.48 1.00 4.90 0

Gigantocellular reticular nucleus GRN Slc6a5-Cre_KF109

160081484 -5.88 2.25 5.00 25

Gigantocellular reticular nucleus GRN Slc6a5-Cre_KF109

267703239 -5.88 2.25 5.00 25

Globus pallidus, external segment GPe C57BL/6J 158373958 -0.34 1.70 3.58 0

Globus pallidus, external segment GPe Htr2a-Cre_KM207

300318924 -0.34 1.70 3.58 0

Globus pallidus, external segment GPe Ntrk1-IRES-Cre 265943460 -0.70 1.80 3.95 0

Page 33: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 33 of 117

Globus pallidus, external segment GPe Ntrk1-IRES-Cre 265944167 -0.34 1.70 3.58 0

Globus pallidus, internal segment GPi Htr2a-Cre_KM207

278501857 -0.70 1.80 3.95 0

Globus pallidus, internal segment GPi Ntrk1-IRES-Cre 292960052 -1.34 1.75 4.50 0

Globus pallidus, internal segment GPi Rbp4-Cre_KL100 305024724 -1.70 2.75 5.25 0

Gracile nucleus GR C57BL/6J 114400640 0.00 calamus

(-7.20 bregma)

0.25 0.15 0

Gracile nucleus GR Erbb4-2A-CreERT2

268321221 0.20 calamus

(-7.00 bregma)

0.25 0.15 0

Gracile nucleus GR Sst-IRES-Cre 300843120 0.2 calamus

(-7.00 bregma)

0.25 0.15 0

Gustatory areas GU C57BL/6J 180404418 0.38 3.60 2.35 0

Gustatory areas GU C57BL/6J 272737914 1.10 3.25, 3.00 1.90, 2.35

0

Gustatory areas GU Cux2-IRES-Cre 264076854 1.78 2.40, 2.80 2.25 0

Gustatory areas GU Nr5a1-Cre 177892379 1.10 3.25, 3.00 1.90, 2.35

0

Gustatory areas GU Rbp4-Cre_KL100 272928602 1.10 3.25, 3.00 1.90, 2.35

0

Hypoglossal nucleus XII C57BL/6J 127350480 -0.16 calamus

(-7.48 bregma)

0.25 0.65 0

Page 34: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 34 of 117

Hypoglossal nucleus XII Chat-IRES-Cre 165973664 -0.16 calamus

(-7.48 bregma)

0.25 0.65 0

Hypoglossal nucleus XII Chat-IRES-Cre 177606140 -0.16 calamus

(-7.48 bregma)

0.35 0.65 0

Hypoglossal nucleus XII Scnn1a-Tg2-Cre 177904363 -0.16 calamus

(-7.48 bregma)

0.35 0.65 0

Inferior colliculus IC C57BL/6J 147162027 -4.96 1.40 0.85 0

Inferior colliculus IC Nos1-CreERT2 299761293 -5.02 0.50 0.65 0

Inferior colliculus IC Pdzk1ip1-Cre_KD31

183375545 -5.20 1.25 1.30 0

Inferior colliculus IC Pdzk1ip1-Cre_KD31

266966337 -5.02 0.50 0.65 0

Inferior colliculus IC Slc17a6-IRES-Cre

287448038 -5.20 1.25 1.30 0

Inferior colliculus IC Slc17a6-IRES-Cre

294174290 -4.48 0.50 1.85 0

Inferior colliculus IC Sst-IRES-Cre 305446876 -4.72 1.25 1.10 0

Inferior colliculus, central nucleus ICc C57BL/6J 113368085 -5.20 1.25 1.30 0

Inferior colliculus, central nucleus ICc Slc17a6-IRES-Cre

287452840 -4.72 1.25 1.10 0

Inferior colliculus, dorsal nucleus ICd C57BL/6J 116905391 -5.02 0.50 0.65 0

Inferior colliculus, external nucleus ICe C57BL/6J 100141596 -4.36 1.59 1.87 0

Inferior colliculus, external nucleus ICe Chrna2-Cre_OE25

304857992 -5.20 1.25 1.30 0

Page 35: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 35 of 117

Inferior colliculus, external nucleus ICe Nxph4-2A-CreERT2

287714197 -4.36 1.59 1.87 0

Inferior colliculus, external nucleus ICe Pvalb-IRES-Cre 277959325 -5.20 1.25 1.30 0

Inferior colliculus, external nucleus ICe Slc17a6-IRES-Cre

294199114 -4.36 1.87 2.58 0

Inferior colliculus, external nucleus ICe Sst-IRES-Cre 305447664 -5.20 1.25 2.80 0

Inferior olivary complex IO Calb2-IRES-Cre 182890735 -0.24 calamus

(-7.56 bregma)

1.12 2.30 0

Inferior olivary complex IO Crh-IRES-Cre (BL)

167665302 0.00 calamus

(-7.32 bregma)

0.10 2.40 0

Inferior olivary complex IO Crh-IRES-Cre (ZJH)

292622743 -0.24 calamus

(-7.56 Bregma)

1.12 2.30 0

Infralimbic area ILA C57BL/6J 157556400 1.70 0.40 2.00 0

Infralimbic area ILA Chrna2-Cre_OE25

298272589 1.70 0.40 2.00 0

Infralimbic area ILA Cux2-IRES-Cre 287494320 -4.04 4.00 0.35 30

Infralimbic area ILA Grp-Cre_KH288 266583498 1.70 0.40 2.00 0

Infralimbic area ILA Oxtr-Cre_ON66 294399325 1.70 0.40 2.00 0

Infralimbic area ILA Rbp4-Cre_KL100 286313491 1.70 0.40 2.00 0

Infralimbic area ILA Syt17-Cre_NO14 299653551 1.70 0.40 2.00 0

Infralimbic area ILA Syt6-Cre_KI148 177889243 2.10 0.06, 0.33 1.50 0

Infralimbic area ILA Ucn3-Cre_KF43 266913950 2.68 0.65 1.64 0

Page 36: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 36 of 117

Interanterodorsal nucleus of the thalamus

IAD Crh-IRES-Cre (BL)

264707643 -5.52 0.88 2.71 0

Intercalated amygdalar nucleus IA C57BL/6J 146012934 -0.94 2.60 4.60 0

Interfascicular nucleus raphe IF C57BL/6J 120572378 -3.52 0.08 4.30 0

Interfascicular nucleus raphe IF Calb2-IRES-Cre 310176384 -3.28 0.36 4.13 0

Interfascicular nucleus raphe IF Erbb4-2A-CreERT2

267538735 -3.52 0.08 4.30 0

Interfascicular nucleus raphe IF Gad2-IRES-Cre 164985329 -3.52 0.08 4.30 0

Interfascicular nucleus raphe IF Slc17a6-IRES-Cre

287808449 -3.52 0.08 4.30 0

Intergeniculate leaflet of the lateral geniculate complex

IGL Gad2-IRES-Cre 293942897 -2.30 2.55 3.00 0

Intergeniculate leaflet of the lateral geniculate complex

IGL Plxnd1-Cre 301991713 -2.00 2.15 2.60 0

Intermediate reticular nucleus IRN C57BL/6J 126189322 -6.64 1.25 4.60 0

Intermediate reticular nucleus IRN C57BL/6J 126709328 -6.64 1.25 4.00 0

Intermediate reticular nucleus IRN C57BL/6J 127041126 0.00 calamus

(-7.32 bregma)

1.00 1.36 0

Intermediate reticular nucleus IRN C57BL/6J 158838128 -5.34 0.65 4.07 0

Intermediate reticular nucleus IRN C57BL/6J 159021559 -0.24 calamus

(-7.56 bregma)

1.12 2.28 0

Intermediate reticular nucleus IRN C57BL/6J 159024474 -0.24 calamus

(-7.56 bregma)

1.35 1.35 0

Intermediate reticular nucleus IRN C57BL/6J 175265301 -5.34 0.65 4.10 0

Page 37: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 37 of 117

Intermediate reticular nucleus IRN Dbh-Cre_KH212 287029186 -6.48 1.00 4.90 0

Intermediate reticular nucleus IRN Plxnd1-Cre 301464820 -6.00 1.15 4.57 0

Intermediate reticular nucleus IRN Pnmt-Cre 156253662 -6.24 0.85 4.30 0

Intermediate reticular nucleus IRN Slc17a6-IRES-Cre

302016107 -6.24 0.85 4.40 0

Intermediate reticular nucleus IRN Slc18a2-Cre_OZ14

265633461 -0.24 calamus

(-7.56 bregma)

1.25 1.45 0

Intermediate reticular nucleus IRN Slc6a5-Cre_KF109

160153696 -5.34 1.11 4.80 0

Intermediodorsal nucleus of the thalamus

IMD Grm2-Cre_MR90 182185289 -1.70 0.20 3.25 0

Intermediodorsal nucleus of the thalamus

IMD Lypd6-Cre_KL156

298001595 -1.70 0.20 3.25 0

Intermediodorsal nucleus of the thalamus

IMD Plxnd1-Cre 293365328 -1.06 0.20 3.40 0

Intermediodorsal nucleus of the thalamus

IMD Syt17-Cre_NO14 286646170 -1.06 0.20 3.40 0

Intermediodorsal nucleus of the thalamus

IMD Ucn3-Cre_KF43 179902786 -1.06 1.15 3.35 20

Interpeduncular nucleus IPN C57BL/6J 175158844 -3.45 0.15 4.30 0

Interpeduncular nucleus IPN Drd3-Cre_KI196 304859407 -2.70 0.13 5.20 0

Interpeduncular nucleus IPN Gad2-IRES-Cre 303474463 -3.52 0.08 4.30 0

Interpeduncular nucleus IPN Nos1-CreERT2 299761999 -3.52 0.08 4.30 0

Interpeduncular nucleus IPN Ntrk1-IRES-Cre 184212995 -3.52 0.08 4.30 0

Interpeduncular nucleus IPN Slc32a1-IRES-Cre

171019710 -3.52 0.08 4.30 0

Interposed nucleus IP C57BL/6J 120493315 -6.24 1.50 2.25 0

Page 38: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 38 of 117

Interposed nucleus IP Gabrr3-Cre_KC112

168664192 -5.20 1.25 2.80 0

Interposed nucleus IP Gad2-IRES-Cre 293550435 -6.24 1.50 2.60 0

Interposed nucleus IP Gpr26-Cre_KO250

265928489 -6.24 1.50 2.60 0

Interposed nucleus IP Gpr26-Cre_KO250

304996627 -5.88 2.25 2.19 0

Interposed nucleus IP Ntsr1-Cre_GN220

264096952 -6.24 1.50 2.60 0

Interposed nucleus IP Slc17a6-IRES-Cre

304474221 -6.24 1.50 2.60 0

Interposed nucleus IP Slc32a1-IRES-Cre

304537794 -6.24 1.50 2.60 0

Lateral amygdalar nucleus LA C57BL/6J 120762196 -1.46 3.75 3.40 0

Lateral amygdalar nucleus LA Cux2-CreERT2 310437091 -1.46 3.75 3.40 0

Lateral amygdalar nucleus LA Gad2-IRES-Cre 293975337 -1.46 3.55 3.70 0

Lateral amygdalar nucleus LA Ppp1r17-Cre_NL146

287027773 -1.46 3.55 3.70 0

Lateral dorsal nucleus of thalamus LD C57BL/6J 113784293 -1.22 1.25 2.44 0

Lateral dorsal nucleus of thalamus LD C57BL/6J 272967913 -1.82 1.25 2.50 0

Lateral dorsal nucleus of thalamus LD C57BL/6J 272969333 -1.22 1.25 2.45 0

Lateral dorsal nucleus of thalamus LD Calb2-IRES-Cre 298833033 -0.94 1.12 2.60 0

Lateral dorsal nucleus of thalamus LD Gal-Cre_KI87 113554008 -1.22 1.25 2.44 0

Lateral dorsal nucleus of thalamus LD Prkcd-GluCla-CFP-IRES-Cre

267609756 -0.58 1.00 2.93 0

Lateral dorsal nucleus of thalamus LD Slc17a7-IRES2-Cre

301618828 -2.00 2.15 2.60 0

Lateral habenula LH C57BL/6J 147353537 -1.70 0.42 2.60 0

Page 39: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 39 of 117

Lateral habenula LH Calb2-IRES-Cre 301057735 -1.58 0.68 2.75 0

Lateral habenula LH Grm2-Cre_MR90 292623457 -1.34 0.40 2.70 0

Lateral habenula LH Grm2-Cre_MR90 300236056 -1.70 0.42 2.45 0

Lateral hypothalamic area LHA C57BL/6J 112228391 -1.46 0.10 5.90 0

Lateral hypothalamic area LHA C57BL/6J 112372418 -0.58 3.40 4.94 40

Lateral hypothalamic area LHA C57BL/6J 112425523 -2.30 0.25 4.37 0

Lateral hypothalamic area LHA C57BL/6J 113313632 -0.70 1.12 5.00 0

Lateral hypothalamic area LHA C57BL/6J 113369603 -0.70 1.13 5.40 0

Lateral hypothalamic area LHA C57BL/6J 114046440 -1.34 0.95 4.55 0

Lateral hypothalamic area LHA C57BL/6J 117302771 -0.58 1.75 4.50 0

Lateral hypothalamic area LHA C57BL/6J 127470271 -1.94 0.90 5.00 0

Lateral hypothalamic area LHA C57BL/6J 158258062 -1.46 0.39 5.50 0

Lateral hypothalamic area LHA C57BL/6J 158373181 -0.58 1.75 4.50 0

Lateral hypothalamic area LHA Calb2-IRES-Cre 267213087 -0.94 1.10 4.88 0

Lateral hypothalamic area LHA Crh-IRES-Cre (ZJH)

171068025 0.38 0.50 3.90 0

Lateral hypothalamic area LHA Esr1-2A-Cre 176887774 -1.50 0.78 5.75 0

Lateral hypothalamic area LHA Fezf1-2A-dCre 287667137 -1.06 1.70 5.55 0

Lateral hypothalamic area LHA Hcrt-Cre 298048079 -0.70 1.12 5.00 0

Lateral hypothalamic area LHA Hcrt-Cre 298048787 -1.94 0.90 5.00 0

Lateral hypothalamic area LHA Lepr-IRES-Cre 113225519 -1.34 1.00 4.84 0

Lateral hypothalamic area LHA Lepr-IRES-Cre 160296448 -1.90 0.25 5.40 0

Lateral hypothalamic area LHA Lypd6-Cre_KL156

298078515 -2.80 0.80 5.15 0

Page 40: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 40 of 117

Lateral hypothalamic area LHA Lypd6-Cre_KL156

298104533 -2.46 1.00 5.30 0

Lateral hypothalamic area LHA Oxt-IRES-Cre 113037759 -0.70 1.13 5.23 0

Lateral hypothalamic area LHA Oxt-IRES-Cre 265125894 -0.58 1.15 5.50 0

Lateral hypothalamic area LHA Plxnd1-Cre 293368154 -2.46 0.55 5.65 0

Lateral hypothalamic area LHA Pmch-Cre 113444277 -1.34 1.00 4.95 0

Lateral hypothalamic area LHA Pmch-Cre 113506174 -1.06 1.20 5.00 0

Lateral hypothalamic area LHA Pmch-Cre 142653395 -0.70 1.12 5.00 0

Lateral hypothalamic area LHA Pmch-Cre 171020416 -0.70 1.12 5.00 0

Lateral hypothalamic area LHA Ppp1r17-Cre_NL146

267928135 -1.34 1.00 4.84 0

Lateral hypothalamic area LHA Ppp1r17-Cre_NL146

278508779 -0.70 1.12 5.00 0

Lateral hypothalamic area LHA Ppp1r17-Cre_NL146

278510197 -0.94 1.10 4.88 0

Lateral hypothalamic area LHA Ppp1r17-Cre_NL146

286882342 -1.50 0.35 5.30 0

Lateral hypothalamic area LHA Sim1-Cre 156195758 -1.94 0.90 5.00 0

Lateral hypothalamic area LHA Sim1-Cre 165035106 -1.34 1.00 4.84 0

Lateral hypothalamic area LHA Sim1-Cre 170860092 -0.70 1.12 5.00 0

Lateral hypothalamic area LHA Sim1-Cre 177890956 -0.58 0.20 4.75 0

Lateral hypothalamic area LHA Slc32a1-IRES-Cre

304674547 -1.34 1.00 4.84 0

Lateral hypothalamic area LHA Tac2-IRES2-Cre 293254286 -0.46 1.25 4.88 0

Lateral hypothalamic area LHA Tac2-IRES2-Cre 300927483 -1.50 0.35 5.30 0

Lateral posterior nucleus of the thalamus

LP C57BL/6J 113846682 -3.16 2.10 2.85 0

Page 41: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 41 of 117

Lateral posterior nucleus of the thalamus

LP C57BL/6J 114399224 -2.18 1.45 2.44 0

Lateral posterior nucleus of the thalamus

LP C57BL/6J 266585624 -1.82 1.25 2.60 0

Lateral posterior nucleus of the thalamus

LP C57BL/6J 272873704 -3.16 2.05 2.65 0

Lateral posterior nucleus of the thalamus

LP Calb2-IRES-Cre 183282261 -1.22 1.25 2.44 0

Lateral posterior nucleus of the thalamus

LP Calb2-IRES-Cre 183282970 -2.18 1.45 2.44 0

Lateral posterior nucleus of the thalamus

LP Grik4-Cre 167439900 -2.18 1.45 2.44 0

Lateral posterior nucleus of the thalamus

LP Grik4-Cre 183175010 -2.18 1.45 2.44 0

Lateral posterior nucleus of the thalamus

LP Nos1-CreERT2 293888501 -3.16 2.10 2.85 0

Lateral posterior nucleus of the thalamus

LP Plxnd1-Cre 301466249 -2.30 2.00 2.60 0

Lateral posterior nucleus of the thalamus

LP Prkcd-GluCla-CFP-IRES-Cre

267608343 -1.22 1.25 2.44 0

Lateral posterior nucleus of the thalamus

LP Prkcd-GluCla-CFP-IRES-Cre

292319865 -2.30 2.00 2.60 0

Lateral posterior nucleus of the thalamus

LP Vipr2-Cre_KE2 182805258 -3.16 2.10 2.85 0

Lateral preoptic area LPO C57BL/6J 113553300 0.62 1.20 4.85 0

Lateral preoptic area LPO C57BL/6J 113554719 0.50 0.81 4.84 0

Lateral preoptic area LPO C57BL/6J 113783321 1.18 0.60 4.15 0

Lateral preoptic area LPO C57BL/6J 146470726 -2.80 4.40 2.25 0

Lateral preoptic area LPO C57BL/6J 175263771 0.50 0.80 5.00 0

Page 42: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 42 of 117

Lateral preoptic area LPO Crh-IRES-Cre (BL)

293114113 -4.36 0.30 4.55 0

Lateral preoptic area LPO Ntrk1-IRES-Cre 292961470 0.50 0.90 4.85 0

Lateral preoptic area LPO Ntrk1-IRES-Cre 309794438 0.74 0.50 4.25 0

Lateral preoptic area LPO Slc17a6-IRES-Cre

293942188 0.50 0.81 4.84 0

Lateral reticular nucleus, magnocellular part

LRNm Crh-IRES-Cre (BL)

277906744 -0.34 calamus

(-7.64 bregma)

1.15 2.30 0

Lateral reticular nucleus, magnocellular part

LRNm Pvalb-IRES-Cre 286725359 -0.24 calamus

(-7.56 Bregma)

1.12 2.30 0

Lateral reticular nucleus, magnocellular part

LRNm Scnn1a-Tg2-Cre 263553934 -0.24 calamus

(-7.56 bregma)

1.12 2.30 0

Lateral reticular nucleus, magnocellular part

LRNm Th-Cre_FI172 304969906 -0.24 calamus

(-7.56 Bregma)

1.12 2.30 0

Lateral septal nucleus LS C57BL/6J 272917631 0.38 0.30 2.30 0

Lateral septal nucleus LS Efr3a-Cre_NO108

300164356 0.86 0.45 2.91 0

Lateral septal nucleus, caudal (caudodorsal) part

LSc Slc18a2-Cre_OZ14

301672044 0.38 0.30 2.30 0

Lateral septal nucleus, caudal (caudodorsal) part

LSc Sst-Cre-D 160294327 0.38 0.30 2.30 0

Lateral septal nucleus, caudal (caudodorsal) part

LSc Sst-IRES-Cre 300841699 0.38 0.30 2.30 0

Page 43: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 43 of 117

Lateral septal nucleus, rostral (rostroventral) part

LSr C57BL/6J 100141435 0.86 0.45 2.91 0

Lateral septal nucleus, rostral (rostroventral) part

LSr C57BL/6J 120436988 0.38 0.30 2.30 0

Lateral septal nucleus, rostral (rostroventral) part

LSr Cart-Tg1-Cre 178486024 -1.50 0.35 5.20 0

Lateral septal nucleus, rostral (rostroventral) part

LSr Gnrh1-Cre 160398593 0.98 0.25 4.60 0

Lateral septal nucleus, rostral (rostroventral) part

LSr Ppp1r17-Cre_NL146

267810394 0.86 0.45 2.91 0

Lateral septal nucleus, rostral (rostroventral) part

LSr Prkcd-GluCla-CFP-IRES-Cre

265946352 0.86 0.45 2.91 0

Lateral septal nucleus, rostral (rostroventral) part

LSr Slc18a2-Cre_OZ14

301672755 0.86 0.45 2.91 0

Lateral septal nucleus, rostral (rostroventral) part

LSr Th-Cre_FI172 287533790 1.18 0.60 4.15 0

Lateral septal nucleus, ventral part LSv Calb2-IRES-Cre 182887258 0.10 0.40 3.67 0

Lateral vestibular nucleus LAV C57BL/6J 277618054 -6.00 1.40 3.20 0

Lateral vestibular nucleus LAV Slc17a6-IRES-Cre

300687607 -6.48 1.25 3.25 0

Lateral visual area VISl A930038C07Rik-Tg1-Cre

166461899 -4.16 3.75 0.81 0

Lateral visual area VISl A930038C07Rik-Tg1-Cre

264630019 -4.16 3.95 0.85 0

Lateral visual area VISl C57BL/6J 100141796 -4.04 4.00 0.35, 0.75

0

Lateral visual area VISl C57BL/6J 112373830 -4.60 3.80 0.45 30

Lateral visual area VISl Chrna2-Cre_OE25

299782273 -4.04 4.00 0.35, 0.75

30

Lateral visual area VISl Cux2-IRES-Cre 272736450 -4.16 3.95 0.85 0

Page 44: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 44 of 117

Lateral visual area VISl Nr5a1-Cre 286554724 -4.04 4.00 0.35, 0.75

30

Lateral visual area VISl Ntsr1-Cre_GN220

159320367 -4.16 3.75 0.81 0

Lateral visual area VISl Scnn1a-Tg3-Cre 184075100 -4.04 4.00 0.35, 0.75

20

Lateral visual area VISl Syt6-Cre_KI148 267031577 -4.04 3.80 1.90 0

Laterodorsal tegmental nucleus LDT Slc18a2-Cre_OZ14

301671287 -5.34 0.50 2.70 0

Lobule II CENT2 C57BL/6J 119848249 -5.68 0.50 2.32 0

Lobule II CENT2 C57BL/6J 146012184 -5.20 0.17 2.70 0

Lobule II CENT2 C57BL/6J 147134401 -5.40 0.68 2.75 0

Lobule II CENT2 C57BL/6J 156872043 -5.40 0.50 2.75 0

Lobule III CENT3 C57BL/6J 127398177 -5.68 0.50 1.45 0

Lobule III CENT3 Nxph4-2A-CreERT2

287713485 -6.36 0.75 2.10 0

Lobule III CENT3 Pcp2-Cre_GN135

147708352 -6.24 0.50 0.94 0

Lobule III CENT3 Slc17a6-IRES-Cre

304543821 -6.36 0.75 2.10 0

Lobule IV CUL4 Scnn1a-Tg3-Cre 113888575 -4.48 2.40 2.70 0

Lobule IV CUL4 Scnn1a-Tg3-Cre 156255078 -4.60 2.40 2.55 0

Lobules IV-V CUL4,5 C57BL/6J 112424102 -6.24 0.50 0.94 0

Lobules IV-V CUL4,5 C57BL/6J 114473794 -5.90 0.50 0.40 0

Lobules IV-V CUL4,5 Efr3a-Cre_NO108

299732033 -5.20 1.95 2.85 0

Lobules IV-V CUL4,5 Gabra6-IRES-Cre

181128406 -6.24 0.50 0.94 0

Page 45: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 45 of 117

Lobules IV-V CUL4, 5 Gad2-IRES-Cre 287809155 -6.36 0.75 2.10 0

Lobules IV-V CUL4, 5 Grm2-Cre_MR90 292531359 -6.24 0.50 0.94 0

Lobules IV-V CUL4,5 Pvalb-IRES-Cre 167202174 -6.24 0.50 0.94 0

Locus ceruleus LC C57BL/6J 277618762 -5.52 1.20 3.00 0

Locus ceruleus LC Dbh-Cre_KH212 159510205 -5.52 0.88 2.71 0

Locus ceruleus LC Dbh-Cre_KH212 159942862 -5.20 0.91 3.09 0

Locus ceruleus LC Gal-Cre_KI87 301210208 -5.52 0.88 2.71 0

Magnocellular nucleus MA Chat-IRES-Cre 161460864 0.62 1.20 4.85 0

Magnocellular nucleus MA Gad2-IRES-Cre 302736304 0.62 1.20 4.85 0

Magnocellular reticular nucleus MARN C57BL/6J 121145750 -5.88 2.25 5.00 25

Magnocellular reticular nucleus MARN C57BL/6J 127349111 0.00 calamus

(-7.32 bregma)

0.85 2.05 0

Magnocellular reticular nucleus MARN Gad2-IRES-Cre 302222934 -5.88 2.25 5.30 25

Magnocellular reticular nucleus MARN Gal-Cre_KI87 178283952 -0.24 calamus

(-7.56 bregma)

1.12 2.30 0

Magnocellular reticular nucleus MARN Pvalb-IRES-Cre 278066728 -5.02 0.50 5.70 0

Magnocellular reticular nucleus MARN Slc32a1-IRES-Cre

286647583 -5.02 0.50 5.70 0

Magnocellular reticular nucleus MARN Slc6a5-Cre_KF109

160080778 -5.02 0.50 5.30 0

Main olfactory bulb MOB A930038C07Rik-Tg1-Cre

264631432 4.28 1.20 0.70 0

Main olfactory bulb MOB C57BL/6J 100141222 4.28 0.50 2.31 0

Page 46: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 46 of 117

Main olfactory bulb MOB Cdhr1-Cre_KG66 146859480 4.28 0.50 2.31 0

Main olfactory bulb MOB Cdhr1-Cre_KG66 146921849 4.28 1.20 0.70 0

Main olfactory bulb MOB Cdhr1-Cre_KG66 175728165 3.08 0.45 2.55 0

Main olfactory bulb MOB Cdhr1-Cre_KG66 175731154 3.08 1.00 1.75 0

Main olfactory bulb MOB Gpr26-Cre_KO250

304947087 4.28 0.50 2.31 0

Main olfactory bulb MOB Slc17a6-IRES-Cre

300644693 4.28 0.50 2.31 0

Main olfactory bulb MOB Slc6a3-Cre 166154193 4.28 0.50 2.31 0

Main olfactory bulb MOB Slc6a3-Cre 166156241 4.28 1.20 0.70 0

Main olfactory bulb MOB Slc6a3-Cre 182042349 3.08 0.45 2.55 0

Main olfactory bulb MOB Syt6-Cre_KI148 179642401 2.68 0.45 1.46 0

Medial amygdalar nucleus MEA C57BL/6J 146985623 -0.82 2.20 5.53 0

Medial amygdalar nucleus MEA Cart-Tg1-Cre 182041643 -0.94 1.88 5.20 0

Medial amygdalar nucleus MEA Crh-IRES-Cre (ZJH)

204907355 -1.58 2.60 3.90 0

Medial amygdalar nucleus MEA Etv1-CreERT2 267813932 -1.22 2.34 4.75 0

Medial amygdalar nucleus MEA Fezf1-2A-dCre 267547788 -1.06 1.70 5.55 0

Medial amygdalar nucleus MEA Htr2a-Cre_KM207

293469501 -0.94 1.88 5.20 0

Medial amygdalar nucleus MEA Sim1-Cre 170860801 -1.06 1.70 5.55 0

Medial amygdalar nucleus, anterodorsal part

MEAad C57BL/6J 157550122 -0.70 2.00 5.20 0

Medial amygdalar nucleus, anterodorsal part

MEAad C57BL/6J 180981417 -0.70 2.20 5.00 0

Medial amygdalar nucleus, anterodorsal part

MEAad Cart-Tg1-Cre 168363874 -1.22 2.34 4.75 0

Page 47: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 47 of 117

Medial amygdalar nucleus, anterodorsal part

MEAad Nos1-CreERT2 304694870 -0.94 1.88 5.20 0

Medial amygdalar nucleus, anterodorsal part

MEAad Sim1-Cre 165034344 -1.22 2.34 4.75 0

Medial amygdalar nucleus, anteroventral part

MEAav Adcyap1-2A-Cre 272819994 -1.06 1.70 5.55 0

Medial amygdalar nucleus, anteroventral part

MEAav C57BL/6J 125361005 -0.94 1.88 5.20 0

Medial amygdalar nucleus, anteroventral part

MEAav Fezf1-2A-dCre 309386361 -1.06 1.70 5.55 0

Medial amygdalar nucleus, anteroventral part

MEAav Htr3a-Cre_NO152

305645132 -1.06 1.70 5.55 0

Medial amygdalar nucleus, posterodorsal part

MEApd Crh-IRES-Cre (BL)

277856332 -1.82 2.65 4.25 0

Medial amygdalar nucleus, posterodorsal part

MEApd Slc6a3-Cre 286303000 -1.22 2.34 4.75 0

Medial amygdalar nucleus, posteroventral part

MEApv Sim1-Cre_KJ18 299896150 -1.58 1.80 5.45 0

Medial geniculate complex MG C57BL/6J 180520257 -3.28 2.00 2.80 0

Medial geniculate complex MG Etv1-CreERT2 113165340 -3.16 2.00 2.79 0

Medial geniculate complex MG Gal-Cre_KI87 183329991 -2.30 2.00 2.60 0

Medial geniculate complex MG Slc17a6-IRES-Cre

305269070 -3.16 2.10 2.85 0

Medial geniculate complex, dorsal part MGd Calb2-IRES-Cre 267493760 -2.30 2.00 2.60 0

Medial geniculate complex, ventral part MGv Calb2-IRES-Cre 299996344 -3.64 2.40 2.90 0

Medial geniculate complex, ventral part MGv Prkcd-GluCla-CFP-IRES-Cre

178489574 -3.52 2.50 3.50 0

Medial habenula MH Chat-IRES-Cre 268321927 -1.70 0.42 2.45 0

Medial habenula MH Tac1-IRES2-Cre 300843826 -1.70 0.42 2.45 0

Page 48: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 48 of 117

Medial habenula MH Tac2-IRES2-Cre 265287564 -1.58 1.00 2.90 0

Medial mammillary nucleus MM Adcyap1-2A-Cre 307655867 -2.70 0.13 5.20 0

Medial mammillary nucleus MM C57BL/6J 148197327 -2.46 0.55 5.65 0

Medial mammillary nucleus MM Cart-Tg1-Cre 168364580 -2.35 0.13 5.10 0

Medial mammillary nucleus MM Grm2-Cre_MR90 287173396 -2.70 0.13 5.20 0

Medial mammillary nucleus MM Sim1-Cre 127396760 -2.30 0.50 5.20 0

Medial preoptic area MPO Adcyap1-2A-Cre 287246555 0.26 0.04 4.85 0

Medial preoptic area MPO C57BL/6J 119846838 0.26 0.35 4.60 0

Medial preoptic area MPO C57BL/6J 120280191 0.26 0.35 4.60 0

Medial preoptic area MPO C57BL/6J 127909584 0.46 0.50 4.80 0

Medial preoptic area MPO C57BL/6J 146660293 0.50 0.81 4.84 0

Medial preoptic area MPO C57BL/6J 158315810 0.50 0.81 4.84 0

Medial preoptic area MPO C57BL/6J 158738180 0.40 0.70 5.00 0

Medial preoptic area MPO Calb2-IRES-Cre 301061596 0.26 0.35 4.60 0

Medial preoptic area MPO Gad2-IRES-Cre 305270515 0.26 0.35 4.60 0

Medial preoptic area MPO Gal-Cre_KI87 182459635 0.26 0.04 4.85 0

Medial preoptic area MPO Ntrk1-IRES-Cre 277800288 0.98 0.15 4.65 0

Medial preoptic area MPO Slc17a6-IRES-Cre

292123352 0.38 0.70 5.00 0

Medial preoptic nucleus MPN C57BL/6J 126116142 0.38 0.70 5.00 0

Medial preoptic nucleus MPN Gad2-IRES-Cre 293549729 0.50 0.15 4.75 0

Medial preoptic nucleus MPN Gal-Cre_KI87 182460343 0.02 0.25 4.90 0

Medial preoptic nucleus MPN Kiss1-Cre 301989585 0.50 0.15 4.75 0

Page 49: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 49 of 117

Medial preoptic nucleus MPN Tac1-IRES2-Cre 294355509 0.26 0.35 4.60 0

Medial pretectal area MPT C57BL/6J 156979283 -2.80 0.25 2.40 0

Medial pretectal area MPT Gad2-IRES-Cre 168361750 -2.30 0.25 5.85 0

Medial septal nucleus MS C57BL/6J 100141597 0.62 0.02 3.40 0

Medial septal nucleus MS C57BL/6J 158257355 1.10 0.25 4.60 0

Medial septal nucleus MS Chat-IRES-Cre 156819600 0.62 0.02 3.40 0

Medial septal nucleus MS Drd3-Cre_KI196 298835859 1.70 0.65 4.03 0

Medial septal nucleus MS Gad2-IRES-Cre 303580293 0.62 0.02 3.40 0

Medial septal nucleus MS Gal-Cre_KI87 113696423 0.62 0.02 3.40 0

Medial septal nucleus MS Gnrh1-Cre 168094300 0.62 0.02 3.40 0

Medial septal nucleus MS Htr2a-Cre_KM207

293434703 1.18 0.25 3.41 0

Medial septal nucleus MS Ntrk1-IRES-Cre 265944939 0.62 0.02 3.40 0

Medial septal nucleus MS Oxtr-Cre_ON66 278259822 0.62 0.01 3.40 0

Medial vestibular nucleus MV C57BL/6J 121146455 -6.12 0.85 3.50 0

Medial vestibular nucleus MV Chrna2-Cre_OE25

303709219 -6.36 0.25 3.55 0

Medial vestibular nucleus MV Ntrk1-IRES-Cre 292960764 -6.12 0.85 3.50 0

Medial vestibular nucleus MV Pnmt-Cre 143512399 -6.12 0.85 3.75 0

Medial vestibular nucleus MV Slc6a5-Cre_KF109

157911126 -6.12 0.85 3.50 0

Medial vestibular nucleus MV Sst-IRES-Cre 300842406 -6.12 0.85 3.50 0

Mediodorsal nucleus of thalamus MD C57BL/6J 114291646 -0.58 0.50 3.43 0

Mediodorsal nucleus of thalamus MD C57BL/6J 156931568 -1.06 1.75 3.15 30

Page 50: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 50 of 117

Mediodorsal nucleus of thalamus MD C57BL/6J 173206592 -0.70 0.70 2.80 0

Mediodorsal nucleus of thalamus MD C57BL/6J 267494468 -1.94 0.50 3.20 0

Mediodorsal nucleus of thalamus MD C57BL/6J 272830456 -0.58 0.62 2.92 0

Mediodorsal nucleus of thalamus MD C57BL/6J 272875132 -1.06 1.15 3.35 20

Mediodorsal nucleus of thalamus MD C57BL/6J 272875838 -1.34 0.40 2.70 0

Mediodorsal nucleus of thalamus MD C57BL/6J 272970747 -1.46 0.10 3.35 0

Mediodorsal nucleus of thalamus MD Calb2-IRES-Cre 183329222 -1.34 0.50 3.40 0

Mediodorsal nucleus of thalamus MD Calb2-IRES-Cre 301060890 -1.34 0.50 3.40 0

Mediodorsal nucleus of thalamus MD Gal-Cre_KI87 116904684 -1.34 0.50 3.40 0

Mediodorsal nucleus of thalamus MD Gal-Cre_KI87 168002780 -0.70 0.60 2.90 0

Mediodorsal nucleus of thalamus MD Grik4-Cre 168300739 -1.46 0.44 3.20 0

Mediodorsal nucleus of thalamus MD Grik4-Cre 168301446 -0.82 0.25 2.80 0

Mediodorsal nucleus of thalamus MD Grp-Cre_KH288 183058837 -1.58 0.68 2.73 0

Mediodorsal nucleus of thalamus MD Ppp1r17-Cre_NL146

268399145 -0.82 0.25 2.80 0

Mediodorsal nucleus of thalamus MD Ppp1r17-Cre_NL146

278400363 -1.46 0.44 3.20 0

Mediodorsal nucleus of thalamus MD Prkcd-GluCla-CFP-IRES-Cre

267607635 -1.46 0.44 3.20 0

Mediodorsal nucleus of thalamus MD Prkcd-GluCla-CFP-IRES-Cre

267928844 -0.82 0.25 2.80 0

Mediodorsal nucleus of thalamus MD Slc17a6-IRES-Cre

181895006 -0.70 0.60 2.90 0

Mediodorsal nucleus of thalamus MD Slc17a6-IRES-Cre

294356922 -1.34 0.50 3.40 0

Mediodorsal nucleus of thalamus MD Syt17-Cre_NO14 286485585 -0.70 0.60 3.00 0

Page 51: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 51 of 117

Mediodorsal nucleus of thalamus MD Tac1-IRES2-Cre 300889379 -1.06 1.15 3.35 20

Mediodorsal nucleus of thalamus MD Vipr2-Cre_KE2 268076421 -1.34 0.50 3.40 0

Medullary reticular nucleus, ventral part MDRNv C57BL/6J 127353220 -0.24 calamus

(-7.56 bregma)

1.25 1.43 0

Medullary reticular nucleus, ventral part MDRNv C57BL/6J 273068974 -0.24 calamus

(-7.56 bregma)

0.95 2.30 0

Medullary reticular nucleus, ventral part MDRNv Slc17a6-IRES-Cre

302085421 -6.48 1.00 4.90 0

Midbrain reticular nucleus MRN C57BL/6J 113399428 -3.64 1.50 2.96 0

Midbrain reticular nucleus MRN C57BL/6J 114474520 -3.64 1.50 2.60 0

Midbrain reticular nucleus MRN C57BL/6J 120760759 -3.80 0.87 3.30 0

Midbrain reticular nucleus MRN C57BL/6J 126352037 -4.16 1.00 2.65 0

Midbrain reticular nucleus MRN C57BL/6J 127557915 -3.88 1.30 3.45 0

Midbrain reticular nucleus MRN C57BL/6J 127865687 -3.28 0.60 3.65 0

Midbrain reticular nucleus MRN C57BL/6J 127991964 -4.04 1.80 2.73 0

Midbrain reticular nucleus MRN C57BL/6J 139311530 -3.28 0.91 3.10 0

Midbrain reticular nucleus MRN C57BL/6J 147354242 -2.18 0.80 3.20 0

Midbrain reticular nucleus MRN C57BL/6J 156978574 -4.04 1.80 2.73 0

Midbrain reticular nucleus MRN C57BL/6J 174583904 -2.30 0.60 3.50 0

Midbrain reticular nucleus MRN C57BL/6J 273065264 -3.88 1.30 3.55 0

Midbrain reticular nucleus MRN Erbb4-2A-CreERT2

180522266 -3.28 0.36 4.13 0

Midbrain reticular nucleus MRN Gad2-IRES-Cre 287598261 -3.80 0.04 2.85 0

Page 52: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 52 of 117

Midbrain reticular nucleus MRN Gad2-IRES-Cre 302723204 -3.28 0.60 3.65 0

Midbrain reticular nucleus MRN Htr2a-Cre_KM207

278401778 -2.92 1.25 2.76 0

Midbrain reticular nucleus MRN Pvalb-IRES-Cre 258914806 -3.28 0.60 3.65 0

Midbrain reticular nucleus MRN Th-Cre_FI172 304761539 -3.08 1.25 4.15 0

Midbrain trigeminal nucleus MEV Pvalb-IRES-Cre 267030155 -4.36 0.70 2.20 0

Motor nucleus of trigeminal V Chat-IRES-Cre 166052101 -5.20 1.35 3.10 0

Motor nucleus of trigeminal V Pcdh9-Cre 272829024 -5.20 1.40 3.55 0

Motor nucleus of trigeminal V Pvalb-IRES-Cre 182804552 -4.36 1.60 4.27 0

Motor nucleus of trigeminal V Scnn1a-Tg2-Cre 162019589 -5.20 1.40 3.31 0

Nodulus (X) NOD C57BL/6J 120874405 -6.64 0.50 2.55 0

Nodulus (X) NOD Gad2-IRES-Cre 305293222 -6.12 0.85 3.50 0

Nucleus accumbens ACB C57BL/6J 127255254 1.70 0.80 3.40 0

Nucleus accumbens ACB C57BL/6J 146045723 1.54 1.13 4.85 0

Nucleus accumbens ACB C57BL/6J 175373569 1.18 1.25 3.90 0

Nucleus accumbens ACB Calb2-IRES-Cre 264874516 2.10 0.75 4.05 0

Nucleus accumbens ACB Drd1a-Cre 168614604 1.18 0.60 4.15 0

Nucleus accumbens ACB Drd1a-Cre 168615344 1.70 0.80 3.40 0

Nucleus accumbens ACB Drd1a-Cre 170785775 1.54 1.13 4.85 0

Nucleus accumbens ACB Drd2-Cre_ER44 158020947 1.18 1.25 3.80 0

Nucleus accumbens ACB Drd2-Cre_ER44 167904966 1.54 1.13 4.85 0

Nucleus accumbens ACB Drd2-Cre_ER44 175732001 1.70 0.65 4.00 0

Nucleus accumbens ACB Drd3-Cre_KI196 300078901 0.86 0.50 3.90 0

Page 53: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 53 of 117

Nucleus accumbens ACB Drd3-Cre_KI196 300110369 -0.10 2.55 4.00 30

Nucleus accumbens ACB Gpr26-Cre_KO250

286486329 2.10 0.75 4.20 0

Nucleus accumbens ACB Kcnc2-Cre 171411651 2.34 0.40 4.00 0

Nucleus accumbens ACB Ntrk1-IRES-Cre 265136608 1.18 0.60 4.15 0

Nucleus accumbens ACB Ntrk1-IRES-Cre 287993060 1.70 0.65 4.03 0

Nucleus ambiguus AMB Chat-IRES-Cre 264321572 -0.24 calamus

(-7.56 bregma)

1.25 1.45 0

Nucleus accumbens ACB Ntrk1-IRES-Cre 293008559 1.10 1.50 5.15 0

Nucleus accumbens ACB Ntrk1-IRES-Cre 309739641 1.18 1.25 3.80 0

Nucleus accumbens ACB Ntrk1-IRES-Cre 309740347 1.70 0.80 3.40 0

Nucleus incertus NI Ntrk1-IRES-Cre 265930674 -4.84 0.22 3.75 0

Nucleus incertus NI Ntrk1-IRES-Cre 277799582 -4.84 0.22 3.75 0

Nucleus of Darkschewitsch ND Pdzk1ip1-Cre_KD31

267029447 -3.28 0.20 3.10 0

Nucleus of reunions RE Adcyap1-2A-Cre 204832205 -0.58 0.17 4.40 0

Nucleus of reunions RE C57BL/6J 113504763 -0.58 0.17 4.40 0

Nucleus of reunions RE C57BL/6J 174957972 -0.58 0.20 4.05 0

Nucleus of reunions RE C57BL/6J 175019536 -1.22 0.30 4.15 0

Nucleus of reunions RE C57BL/6J 175374982 -1.46 0.30 5.35 0

Nucleus of reunions RE Calb2-IRES-Cre 184158290 -0.58 0.17 4.20 0

Nucleus of reunions RE Cart-Tg1-Cre 265286700 -0.58 0.17 4.40 0

Nucleus of reunions RE Htr2a-Cre_KM207

278500868 -0.22 2.25 4.03 30

Page 54: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 54 of 117

Nucleus of reunions RE Prkcd-GluCla-CFP-IRES-Cre

265947058 -0.58 0.17 4.40 0

Nucleus of reunions RE Rasgrf2-2A-dCre 310976160 -0.58 0.20 4.75 0

Nucleus of reunions RE Slc17a6-IRES-Cre

304617742 -0.80 0.25 4.85 0

Nucleus of reunions RE Ucn3-Cre_KF43 167025578 -0.94 0.25 4.52 0

Nucleus of the brachium of the inferior colliculus

NB Pdzk1ip1-Cre_KD31

159995481 -4.04 1.80 2.73 0

Nucleus of the lateral lemniscus NLL C57BL/6J 119846129 -4.60 2.40 2.55 0

Nucleus of the lateral lemniscus NLL Scnn1a-Tg3-Cre 156313344 -4.24 2.36 3.58 0

Nucleus of the lateral lemniscus NLL Sst-IRES-Cre 309385637 -3.88 1.30 3.45 0

Nucleus of the lateral lemniscus, ventral part

NLLv Pdzk1ip1-Cre_KD31

157766259 -4.36 1.60 4.27 0

Nucleus of the lateral olfactory tract NLOT C57BL/6J 138058320 -0.10 2.00 5.07 0

Nucleus of the lateral olfactory tract NLOT Sim1-Cre 159151138 -0.46 2.20 5.22 0

Nucleus of the lateral olfactory tract NLOT Slc17a6-IRES-Cre

294174996 -0.46 2.20 5.22 0

Nucleus of the optic tract NOT C57BL/6J 126523791 -2.80 1.00 2.15 0

Nucleus of the optic tract NOT C57BL/6J 158915602 -2.80 1.00 2.00 0

Nucleus of the posterior commissure NPC C57BL/6J 158737454 -2.18 0.80 3.20 0

Nucleus of the solitary tract NTS C57BL/6J 159648854 0.10 calamus

(-7.10 bregma)

0.25 0.25 0

Nucleus of the solitary tract NTS Gad2-IRES-Cre 302050617 0.2 calamus

(-7.00 bregma)

0.25 0.15 0

Page 55: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 55 of 117

Nucleus of the solitary tract NTS Gal-Cre_KI87 175816975 0.20 calamus

(-7.00 bregma)

0.25 0.15 0

Nucleus of the solitary tract NTS Pnmt-Cre 155735108 0.00 calamus

(-7.20 bregma)

0.25 0.15 0

Nucleus of the solitary tract NTS Rasgrf2-2A-dCre 310853453 0.20 0.25 0.15 0

Nucleus of the solitary tract NTS Slc6a5-Cre_KF109

128003477 0.00 calamus

(-7.20 bregma)

0.25 0.15 0

Nucleus of the solitary tract NTS Tac1-IRES2-Cre 180525136 0.20 calamus

(-7.00 bregma)

0.25 0.15 0

Nucleus prepositus PRP C57BL/6J 127908173 -6.36 0.25 3.55 0

Nucleus raphe magnus RM C57BL/6J 147159899 -5.88 2.25 5.30 25

Nucleus raphe magnus RM C57BL/6J 175264587 -4.16 0.25 5.50 0

Nucleus raphe obscurus RO Crh-IRES-Cre (ZJH)

267153115 0.00 calamus

(-7.32 bregma)

0.00 1.20 0

Nucleus raphe obscurus RO Crh-IRES-Cre (ZJH)

301875208 -6.64 0.78 4.80 10

Nucleus raphe obscurus RO Gal-Cre_KI87 300209456 -6.64 0.78 4.80 10

Nucleus raphe obscurus RO Slc18a2-Cre_OZ14

292794673 0.00 calamus

(-7.32 bregma)

0.05 1.00 0

Page 56: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 56 of 117

Nucleus raphe obscurus RO Slc6a4-Cre_ET33

133286781 0.00 calamus

(-7.32 bregma)

0.00 1.00 0

Nucleus raphe obscurus RO Slc6a4-Cre_ET33

141603895 -6.64 0.78 4.80 10

Nucleus raphe obscurus RO Slc6a4-CreERT2_EZ13

167212217 -6.64 0.78 4.80 10

Nucleus raphe obscurus RO Slc6a4-CreERT2_EZ13

168227692 0.00 calamus

(-7.32 bregma)

0.00 1.00 0

Nucleus raphe pontis RPO Cnnm2-Cre_KD18

167376068 -4.72 0.25 4.40 0

Nucleus raphe pontis RPO Slc18a2-Cre_OZ14

287095785 -4.84 0.22 3.75 0

Nucleus raphe pontis RPO Slc6a4-Cre_ET33

267958444 -4.84 0.22 3.75 0

Oculomotor nucleus III C57BL/6J 121509005 -4.16 0.14 2.99 0

Oculomotor nucleus III Chat-IRES-Cre 177460028 -4.04 0.10 3.00 0

Oculomotor nucleus III Htr3a-Cre_NO152

311845265 -4.04 0.10 3.00 0

Oculomotor nucleus III Pvalb-IRES-Cre 266099165 -4.24 0.52 2.86 10

Olfactory tubercle OT C57BL/6J 114755099 2.34 0.40 4.00 0

Olfactory tubercle OT C57BL/6J 147632458 1.10 1.50 5.25 0

Olfactory tubercle OT C57BL/6J 157659671 1.54 1.15 5.00 0

Olfactory tubercle OT Drd2-Cre_ER44 167904255 1.10 1.50 5.15 0

Olfactory tubercle OT Ntrk1-IRES-Cre 292962283 1.54 1.13 4.85 0

Olivary pretectal nucleus OP C57BL/6J 113442864 -2.54 0.70 2.24 0

Page 57: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 57 of 117

Olivary pretectal nucleus OP Pdzk1ip1-Cre_KD31

182031296 -2.35 0.70 2.24 0

Orbital area ORB Chrna2-Cre_OE25

297892843 1.00 0.75 0.30, 0.75

0

Orbital area, lateral part ORBl A930038C07Rik-Tg1-Cre

168164972 2.80 1.25 1.30, 1.67

0

Orbital area, lateral part ORBl C57BL/6J 112306316 2.80 1.25 1.30, 1.67

0

Orbital area, lateral part ORBl Chrna2-Cre_OE25

278174451 2.80 1.25 1.30, 1.67

0

Orbital area, lateral part ORBl Cux2-IRES-Cre 183471174 2.80 1.25 1.30 0

Orbital area, lateral part ORBl Efr3a-Cre_NO108

298230624 2.80 1.25 1.30, 1.67

0

Orbital area, lateral part ORBl Gpr26-Cre_KO250

265713683 2.80 1.25 1.30, 1.67

0

Orbital area, lateral part ORBl Grm2-Cre_MR90 264708349 2.80 1.25 1.30 0

Orbital area, lateral part ORBl Grp-Cre_KH288 288324211 2.80 1.25 1.30, 1.67

0

Orbital area, lateral part ORBl Nos1-CreERT2 268319809 2.80 1.25 1.30, 1.67

0

Orbital area, lateral part ORBl Nos1-CreERT2 293889216 2.80 1.25 1.30, 1.67

0

Orbital area, lateral part ORBl Nr5a1-Cre 159887627 -2.54 1.75 0.20, 0.55

0

Orbital area, lateral part ORBl Oxtr-Cre_ON66 294311830 2.80 1.25 1.30, 1.67

0

Orbital area, lateral part ORBl Rasgrf2-2A-dCre 303783725 2.80 1.25 1.30 0

Orbital area, lateral part ORBl Rbp4-Cre_KL100 156741826 2.80 1.25 1.30, 1.67

0

Orbital area, lateral part ORBl Syt6-Cre_KI148 126353451 2.80 1.25 1.30, 1.67

0

Page 58: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 58 of 117

Orbital area, lateral part ORBl Tlx3-Cre_PL56 293433283 2.80 1.25 1.30, 1.67

0

Orbital area, medial part ORBm A930038C07Rik-Tg1-Cre

283019341 2.68 0.05, 0.45 1.46 0

Orbital area, medial part ORBm C57BL/6J 126860974 2.68 0.05, 0.45 1.46 0

Orbital area, medial part ORBm Chrna2-Cre_OE25

298274021 2.10 0.06, 0.33 1.50 0

Orbital area, medial part ORBm Crh-IRES-Cre (BL)

277855624 2.68 0.65 1.84 0

Orbital area, medial part ORBm Cux2-IRES-Cre 272781246 2.68 0.05, 0.45 1.46 0

Orbital area, medial part ORBm Cux2-IRES-Cre 293471629 2.68 0.05, 0.35 1.45 0

Orbital area, medial part ORBm Efr3a-Cre_NO108

286648290 2.68 0.05, 0.45 1.46 0

Orbital area, medial part ORBm Gpr26-Cre_KO250

301323451 2.68 0.05, 0.35 1.45 0

Orbital area, medial part ORBm Htr2a-Cre_KM207

258916270 2.68 0.05, 0.45 1.46 0

Orbital area, medial part ORBm Htr2a-Cre_KM207

277956496 2.68 0.05, 0.45 1.46 0

Orbital area, medial part ORBm Ntsr1-Cre_GN220

159511623 2.68 0.05, 0.45 1.46 0

Orbital area, medial part ORBm Syt6-Cre_KI148 159209586 2.68 0.05, 0.45 1.46 0

Orbital area, medial part ORBm Syt6-Cre_KI148 265820216 2.68 0.45 1.46 0

Orbital area, ventrolateral part ORBvl C57BL/6J 112423392 2.68 0.65 1.84 0

Orbital area, ventrolateral part ORBvl C57BL/6J 158435116 3.00 1.00 1.90 0

Orbital area, ventrolateral part ORBvl Grp-Cre_KH288 266564027 2.68 0.05, 0.45 1.46 0

Orbital area, ventrolateral part ORBvl Htr2a-Cre_KM207

183618845 2.80 1.25 1.30, 1.67

0

Page 59: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 59 of 117

Orbital area, ventrolateral part ORBvl Rbp4-Cre_KL100 167902586 2.68 0.05, 0.45 1.46 0

Orbital area, ventrolateral part ORBvl Rbp4-Cre_KL100 287769286 -0.10 2.55 4.00 30

Orbital area, ventrolateral part ORBvl Slc32a1-IRES-Cre

309580102 3.08 1.00 1.75 0

Orbital area, ventrolateral part ORBvl Sst-IRES-Cre 288263341 2.80 1.25 1.30, 1.67

0

Orbital area, ventrolateral part ORBvl Syt17-Cre_NO14 127560043 3.20 1.00 1.50 0

Parabigeminal nucleus PBG C57BL/6J 127091083 -4.16 2.25 2.27 0

Parabrachial nucleus PB Adcyap1-2A-Cre 301016900 -5.34 1.50 3.75 0

Parabrachial nucleus PB C57BL/6J 127085717 -5.52 0.88 2.71 0

Parabrachial nucleus PB C57BL/6J 127469566 -5.20 1.25 2.80 0

Parabrachial nucleus PB C57BL/6J 147635309 -4.48 1.15 3.00 0

Parabrachial nucleus PB C57BL/6J 268415561 -5.20 1.40 3.35 0

Parabrachial nucleus PB Calb2-IRES-Cre 183284388 -5.20 1.25 2.80 0

Parabrachial nucleus PB Chat-IRES-Cre 183901489 -5.52 0.88 2.71 0

Parabrachial nucleus PB Chat-IRES-Cre 264565965 -5.20 1.25 2.80 0

Parabrachial nucleus PB Gad2-IRES-Cre 303535149 -5.20 1.25 2.80 0

Parabrachial nucleus PB Grm2-Cre_MR90 292790567 -5.20 1.25 2.80 0

Parabrachial nucleus PB Grp-Cre_KH288 265487421 -5.20 1.25 2.80 0

Parabrachial nucleus PB Htr3a-Cre_NO152

311845972 -5.52 0.88 2.71 0

Parabrachial nucleus PB Nxph4-2A-CreERT2

301991007 -5.34 0.50 2.70 0

Parabrachial nucleus PB Rasgrf2-2A-dCre 313141786 -5.52 0.88 2.71 0

Parabrachial nucleus PB Slc17a6-IRES-Cre

278401072 -5.02 1.20 2.30 0

Page 60: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 60 of 117

Parabrachial nucleus PB Slc17a6-IRES-Cre

305404551 -5.40 0.50 2.75 0

Parabrachial nucleus PB Syt17-Cre_NO14 167442042 -5.34 1.20 2.80 0

Parabrachial nucleus PB Tac1-IRES2-Cre 294356216 -5.20 1.25 2.80 0

Parabrachial nucleus PB Th-Cre_FI172 301016175 -5.20 1.25 2.80 0

Paracentral nucleus PCN Gal-Cre_KI87 168095041 -0.58 0.50 3.43 0

Paracentral nucleus PCN Grm2-Cre_MR90 166264185 -1.34 0.50 3.40 0

Paracentral nucleus PCN Grp-Cre_KH288 183071513 -1.34 0.50 3.40 0

Parafascicular nucleus PF C57BL/6J 266693274 -1.94 0.70 3.60 0

Parafascicular nucleus PF C57BL/6J 272968624 -1.94 0.70 3.50 0

Parafascicular nucleus PF Efr3a-Cre_NO108

299732738 -2.30 0.80 3.20 0

Parafascicular nucleus PF Rbp4-Cre_KL100 300642574 -2.30 0.80 3.20 0

Parafascicular nucleus PF Slc17a6-IRES-Cre

263785543 -2.06 0.45 4.00 0

Parafascicular nucleus PF Slc17a6-IRES-Cre

266412078 0.98 2.65 3.19 0

Parafascicular nucleus PF Slc17a6-IRES-Cre

309580808 -2.18 1.23 3.71 20

Parafascicular nucleus PF Slc18a2-Cre_OZ14

301735080 -2.06 0.45 4.00 0

Parafascicular nucleus PF Vipr2-Cre_KE2 267959197 -1.58 0.68 2.73 0

Paraflocculus PFL C57BL/6J 119847544 -5.40 2.80 2.55 0

Paraflocculus PFL C57BL/6J 120438416 -5.40 2.80 2.55 0

Paraflocculus PFL C57BL/6J 158738894 -4.96 3.00 2.55 0

Paraflocculus PFL Grik4-Cre 182685522 -4.96 3.10 2.65 0

Page 61: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 61 of 117

Paraflocculus PFL Slc32a1-IRES-Cre

304675961 -6.12 2.25 2.90 0

Paragigantocellular reticular nucleus, lateral part

PGRNl C57BL/6J 127042540 -0.24 calamus

(-7.56 bregma)

1.12 2.28 0

Paragigantocellular reticular nucleus, lateral part

PGRNl C57BL/6J 175142304 -0.24 calamus

(-7.56 bregma)

1.12 2.30 0

Paragigantocellular reticular nucleus, lateral part

PGRNl C57BL/6J 181058463 -0.24 calamus

(-7.56 bregma)

1.12 2.30 0

Paragigantocellular reticular nucleus, lateral part

PGRNl Chat-IRES-Cre 161460153 -6.48 1.00 4.82 0

Paragigantocellular reticular nucleus, lateral part

PGRNl Gal-Cre_KI87 182458849 -0.24 calamus

(-7.56 bregma)

1.12 2.30 0

Paragigantocellular reticular nucleus, lateral part

PGRNl Scnn1a-Tg2-Cre 171409520 -0.24 calamus

(-7.56 Bregma)

1.12 2.30 0

Paramedian lobule PRM C57BL/6J 125801739 -7.20 2.25 1.63 0

Parasubiculum PAR C57BL/6J 100148554 -4.48 3.00 3.44 0

Parasubiculum PAR C57BL/6J 120280939 -4.60 2.40 2.55 0

Parasubiculum PAR Cux2-CreERT2 177322126 -4.48 3.00 3.44 0

Parasubiculum PAR Nos1-CreERT2 305071285 4.60 2.40 2.55 0

Parasubiculum PAR Scnn1a-Tg3-Cre 184075807 -4.24 2.50 3.60 0

Parasubiculum PAR Wfs1-Tg2-CreERT2

292530653 -4.24 2.50 3.60 0

Page 62: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 62 of 117

Parasubiculum PAR Wfs1-Tg3-CreERT2

182617186 -4.24 2.36 3.58 0

Parasubthalamic nucleus PSTN A930038C07Rik-Tg1-Cre

264696942 -2.18 1.25 4.95 0

Parasubthalamic nucleus PSTN Ucn3-Cre_KF43 165974379 -2.18 1.25 4.95 0

Parataenial nucleus PT C57BL/6J 123662982 -0.10 2.55 4.00 30

Parataenial nucleus PT C57BL/6J 126843200 -0.48 0.38 3.58 0

Parataenial nucleus PT Cart-Tg1-Cre 176897793 -0.10 2.55 4.00 30

Parataenial nucleus PT Cck-IRES-Cre 159432479 -0.34 0.35 3.58 0

Parataenial nucleus PT Crh-IRES-Cre (BL)

167373923 -0.70 0.50 3.43 0

Parataenial nucleus PT Crh-IRES-Cre (BL)

266839077 0.38 0.50 3.90 0

Parataenial nucleus PT Slc17a6-IRES-Cre

305125123 -0.58 0.50 3.43 0

Parataenial nucleus PT Slc17a6-IRES-Cre

305449231 -0.34 0.35 3.58 0

Paraventricular hypothalamic nucleus PVH Avp-IRES2-Cre 183459175 -0.58 0.20 4.75 0

Paraventricular hypothalamic nucleus PVH Avp-IRES2-Cre 267997620 -0.58 0.20 4.75 0

Paraventricular hypothalamic nucleus PVH Avp-IRES2-Cre 287044088 -0.80 0.25 4.85 0

Paraventricular hypothalamic nucleus PVH Crh-IRES-Cre (BL)

170784358 -0.58 3.40 4.94 40

Paraventricular hypothalamic nucleus PVH Crh-IRES-Cre (BL)

266840498 -0.80 0.25 4.85 0

Paraventricular hypothalamic nucleus PVH Efr3a-Cre_NO108

299759881 -0.58 0.20 4.75 0

Paraventricular hypothalamic nucleus PVH Gad2-IRES-Cre 294040662 0.38 0.02 4.20 0

Paraventricular hypothalamic nucleus PVH Gad2-IRES-Cre 302221478 -0.58 0.20 4.75 0

Page 63: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 63 of 117

Paraventricular hypothalamic nucleus PVH Gal-Cre_KI87 176432524 -0.94 0.25 4.80 0

Paraventricular hypothalamic nucleus PVH Nos1-CreERT2 304998039 -0.58 0.20 4.75 0

Paraventricular hypothalamic nucleus PVH Oxt-IRES-Cre 112951097 -0.58 0.17 4.45 0

Paraventricular hypothalamic nucleus PVH Oxt-IRES-Cre 146983504 -0.58 3.40 4.94 40

Paraventricular hypothalamic nucleus PVH Oxt-IRES-Cre 147051682 -0.94 0.25 4.52 0

Paraventricular hypothalamic nucleus PVH Oxt-IRES-Cre 147136518 -0.58 3.40 4.94 40

Paraventricular hypothalamic nucleus PVH Oxt-IRES-Cre 166532512 -0.94 0.25 4.80 0

Paraventricular hypothalamic nucleus PVH Sim1-Cre 241280698 0.38 0.02 4.20 0

Paraventricular hypothalamic nucleus PVH Tac1-IRES2-Cre 300888673 -0.58 0.20 4.75 0

Paraventricular hypothalamic nucleus PVH Th-Cre_FI172 301014055 -0.58 0.20 4.75 0

Paraventricular hypothalamic nucleus PVH Ucn3-Cre_KF43 127470976 -0.58 3.40 4.94 40

Paraventricular nucleus of the thalamus PVT C57BL/6J 120875111 -1.58 1.00 2.90 20

Paraventricular nucleus of the thalamus PVT C57BL/6J 127255962 -1.06 1.76 3.15 30

Paraventricular nucleus of the thalamus PVT C57BL/6J 147162736 0.14 2.55 4.00 30

Paraventricular nucleus of the thalamus PVT C57BL/6J 180568155 -0.34 0.05 3.45 0

Paraventricular nucleus of the thalamus PVT C57BL/6J 272874417 -0.34 1.15 3.35 20

Paraventricular nucleus of the thalamus PVT Calb2-IRES-Cre 184157585 -1.06 1.15 3.35 20

Paraventricular nucleus of the thalamus PVT Efr3a-Cre_NO108

301209502 -1.06 1.15 3.35 20

Paraventricular nucleus of the thalamus PVT Gal-Cre_KI87 204908781 -0.34 1.15 3.35 20

Paraventricular nucleus of the thalamus PVT Grm2-Cre_MR90 175739791 -1.58 0.35 2.73 0

Paraventricular nucleus of the thalamus PVT Grm2-Cre_MR90 183225830 -0.34 1.15 3.35 20

Paraventricular nucleus of the thalamus PVT Ntrk1-IRES-Cre 263106751 -1.06 1.15 3.35 20

Page 64: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 64 of 117

Paraventricular nucleus of the thalamus PVT Oxtr-Cre_ON66 299448592 -1.06 1.15 3.35 20

Paraventricular nucleus of the thalamus PVT Ppp1r17-Cre_NL146

278510903 -0.46 0.12 3.58 0

Paraventricular nucleus of the thalamus PVT Rasgrf2-2A-dCre 313324664 -1.06 1.15 3.35 20

Paraventricular nucleus of the thalamus PVT Syt17-Cre_NO14 299624500 -1.06 0.20 3.40 0

Parvicellular reticular nucleus PARN C57BL/6J 147354951 -5.80 1.30 4.20 0

Parvicellular reticular nucleus PARN Gad2-IRES-Cre 300208016 -5.80 1.30 4.20 0

Parvicellular reticular nucleus PARN Gad2-IRES-Cre 308981706 -5.80 1.30 4.20 0

Parvicellular reticular nucleus PARN Slc17a6-IRES-Cre

294173584 -6.64 1.25 4.00 0

Pedunculopontine nucleus PPN Chat-IRES-Cre 264566672 -4.48 1.15 3.50 0

Pedunculopontine nucleus PPN Lypd6-Cre_KL156

298079222 -4.48 1.15 3.50 0

Pedunculopontine nucleus PPN Pvalb-IRES-Cre 293252166 -5.20 1.95 3.35 0

Periaqueductal gray PAG Adcyap1-2A-Cre 287247978 -4.24 0.52 2.86 10

Periaqueductal gray PAG C57BL/6J 113096571 -3.80 0.43 2.50 0

Periaqueductal gray PAG C57BL/6J 120761491 -5.02 0.75 1.98 0

Periaqueductal gray PAG C57BL/6J 128002057 -4.84 0.30 3.10 0

Periaqueductal gray PAG C57BL/6J 158376179 -3.52 0.08 4.30 0

Periaqueductal gray PAG C57BL/6J 272829745 -3.28 0.36 4.13 0

Periaqueductal gray PAG Cck-IRES-Cre 183562831 -4.04 0.10 3.00 0

Periaqueductal gray PAG Cck-IRES-Cre 299856390 -3.80 0.04 2.85 0

Periaqueductal gray PAG Dbh-Cre_KH212 300076066 -4.96 0.50 2.60 0

Periaqueductal gray PAG Gad2-IRES-Cre 162020630 -3.80 0.04 2.31 0

Page 65: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 65 of 117

Periaqueductal gray PAG Gad2-IRES-Cre 302053755 -4.36 0.50 2.01 0

Periaqueductal gray PAG Grm2-Cre_MR90 292624169 -5.02 0.75 1.98 0

Periaqueductal gray PAG Lypd6-Cre_KL156

298079928 -4.96 0.50 2.60 0

Periaqueductal gray PAG Nxph4-2A-CreERT2

287712779 -3.80 0.04 2.85 0

Periaqueductal gray PAG Oxtr-Cre_ON66 278261300 -2.30 0.25 3.90 0

Periaqueductal gray PAG Rbp4-Cre_KL100 301540850 -3.80 0.04 2.85 0

Periaqueductal gray PAG Rbp4-Cre_KL100 301541824 -3.80 0.04 2.85 0

Periaqueductal gray PAG Slc6a3-Cre 160538548 -4.36 0.18 2.10 0

Periaqueductal gray PAG Syt6-Cre_KI148 182144176 -1.58 1.00 2.95 20

Periaqueductal gray PAG Syt6-Cre_KI148 304949216 -4.24 0.52 2.86 10

Periaqueductal gray PAG Tac1-IRES2-Cre 180524412 -3.28 0.36 4.13 0

Periaqueductal gray PAG Th-Cre_FI172 272699357 -4.16 0.14 2.99 0

Periaqueductal gray PAG Vip-IRES-Cre 262188772 -4.24 0.52 2.86 10

Periaqueductal gray PAG Vipr2-Cre_KE2 182280207 -3.80 0.04 2.85 0

Perirhinal area PERI C57BL/6J 142656218 -4.24 4.00 1.65 0

Perirhinal area PERI C57BL/6J 180435652 -2.80 4.30 2.05 0

Periventricular hypothalamic nucleus, posterior part

PVp Agrp-IRES-Cre 167117360 -1.90 0.25 5.90 0

Periventricular hypothalamic nucleus, posterior part

PVp Gad2-IRES-Cre 168362462 -2.80 0.25 2.40 0

Periventricular hypothalamic nucleus, posterior part

PVp Gal-Cre_KI87 168005102 -1.90 0.25 5.90 0

Periventricular hypothalamic nucleus, posterior part

PVp Ins2-Cre 298178912 -1.90 0.25 5.90 0

Page 66: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 66 of 117

Periventricular hypothalamic nucleus, posterior part

PVp Lepr-IRES-Cre 179904203 -2.30 0.25 5.85 0

Periventricular hypothalamic nucleus, posterior part

PVp Slc32a1-IRES-Cre

264078267 -2.30 0.25 5.85 0

Periventricular hypothalamic nucleus, preoptic part

PVpo C57BL/6J 114472860 0.26 0.04 4.85 0

Piriform area PIR A930038C07Rik-Tg1-Cre

286775476 -0.34 4.00, 3.75 3.00, 3.25

0

Piriform area PIR Adcyap1-2A-Cre 287225747 -0.46 3.45 4.80 0

Piriform area PIR C57BL/6J 112307046 0.98 2.85 3.14 0

Piriform area PIR C57BL/6J 127907465 1.42 2.80 3.50 0

Piriform area PIR C57BL/6J 131068390 -0.58 3.65 4.10 0

Piriform area PIR C57BL/6J 146857301 -1.46 4.10 3.70 0

Piriform area PIR C57BL/6J 146984209 -1.46 3.95 3.40 0

Piriform area PIR C57BL/6J 157654069 -0.34 3.90 3.20 0

Piriform area PIR C57BL/6J 158374671 -1.46 3.75 3.70 0

Piriform area PIR Cart-Tg1-Cre 171485060 -1.46 3.55 3.70 0

Piriform area PIR Cux2-CreERT2 286728190 -0.22 3.30 3.25 0

Piriform area PIR Cux2-CreERT2 310436191 0.98 2.85 3.14 0

Piriform area PIR Cux2-CreERT2 310439724 -0.46 3.00 4.40 0

Piriform area PIR Drd3-Cre_KI196 300109663 -1.46 4.00 3.70 0

Piriform area PIR Drd3-Cre_KI198 300168916 -1.46 4.00 3.70 0

Piriform area PIR Rbp4-Cre_KL100 298720898 -1.46 4.00 3.70 0

Piriform area PIR Slc32a1-IRES-Cre

305294666 -1.46 4.00 3.70 0

Piriform area PIR Syt17-Cre_NO14 184259031 -1.46 4.00 3.70 0

Page 67: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 67 of 117

Piriform area PIR Syt6-Cre_KI148 159433905 -0.34 4.00, 3.75 3.00, 3.25

0

Piriform area PIR Vip-IRES-Cre 299655676 -1.06 3.00 3.90 0

Piriform area PIR Vip-IRES-Cre 299897573 -0.58 3.65 4.10 0

Piriform-amygdalar area PAA Gad2-IRES-Cre 302740314 -1.70 2.75 5.25 0

Pontine central gray PCG C57BL/6J 142655513 -4.48 0.12 3.77 0

Pontine central gray PCG C57BL/6J 143513811 -5.20 0.06 3.25 0

Pontine central gray PCG C57BL/6J 158434409 -5.20 0.25 4.40 0

Pontine central gray PCG C57BL/6J 158435826 -5.40 0.68 2.90 0

Pontine central gray PCG Crh-IRES-Cre (ZJH)

182224715 -5.52 0.88 2.71 0

Pontine central gray PCG Crh-IRES-Cre (ZJH)

307928463 -4.84 0.22 3.75 0

Pontine central gray PCG Ntrk1-IRES-Cre 262215150 -5.40 0.50 2.75 0

Pontine central gray PCG Sst-IRES-Cre 310377782 -5.20 0.17 3.30 0

Pontine reticular nucleus PRNr C57BL/6J 127223428 -4.36 0.30 4.35 0

Pontine reticular nucleus PRNr C57BL/6J 152995635 -4.48 0.75 4.10 0

Pontine reticular nucleus PRNr C57BL/6J 156930126 -4.36 1.70 4.35 0

Pontine reticular nucleus PRNr Crh-IRES-Cre (ZJH)

310695955 -4.72 0.25 4.40 0

Pontine reticular nucleus PRNr Pvalb-IRES-Cre 258316862 -4.60 0.50 5.30 0

Pontine reticular nucleus PRNr Slc6a5-Cre_KF109

258315443 -4.36 1.60 4.27 0

Pontine reticular nucleus, caudal part PRNc C57BL/6J 125437216 -5.34 0.50 4.07 0

Pontine reticular nucleus, caudal part PRNc C57BL/6J 147633885 -5.34 0.50 4.07 0

Pontine reticular nucleus, caudal part PRNc C57BL/6J 272700063 -4.60 0.75 4.10 0

Page 68: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 68 of 117

Pontine reticular nucleus, caudal part PRNc C57BL/6J 272826010 -4.04 0.25 5.90 0

Pontine reticular nucleus, caudal part PRNc Slc6a5-Cre_KF109

168515225 -4.48 0.75 4.10 0

Pontine reticular nucleus, caudal part PRNc Slc6a5-Cre_KF109

300691325 -4.96 1.05 4.90 0

Pontine reticular nucleus, caudal part PRNc Slc17a6-IRES-Cre

309701202 -4.36 0.30 4.55 0

Posterior amygdalar nucleus PA Vip-IRES-Cre 299656382 -2.54 3.00 4.55 0

Posterior complex of the thalamus PO C57BL/6J 100147785 -2.06 1.25 2.97 0

Posterior complex of the thalamus PO C57BL/6J 146658879 -2.18 1.45 2.64 0

Posterior complex of the thalamus PO C57BL/6J 174781014 -1.70 1.25 3.05 0

Posterior complex of the thalamus PO C57BL/6J 180628971 -1.94 1.60 3.40 0

Posterior complex of the thalamus PO C57BL/6J 180708524 -1.50 1.25 3.05 0

Posterior complex of the thalamus PO Grik4-Cre 183011353 -2.06 1.25 2.97 0

Posterior complex of the thalamus PO Grik4-Cre 267999740 -2.06 1.25 2.97 0

Posterior complex of the thalamus PO Grik4-Cre 292212456 -2.06 1.25 2.97 0

Posterior complex of the thalamus PO Slc17a6-IRES-Cre

305425490 -2.06 1.25 2.97 0

Posterior complex of the thalamus PO Slc18a2-Cre_OZ14

182892855 -1.82 1.50 3.25 0

Posterior complex of the thalamus PO Slc18a2-Cre_OZ14

301674988 -1.82 1.60 3.30 0

Posterior hypothalamic nucleus PH C57BL/6J 100141434 -1.34 1.00 4.89 0

Posterior hypothalamic nucleus PH C57BL/6J 114045733 -2.35 0.13 4.98 0

Posterior hypothalamic nucleus PH C57BL/6J 127710392 -1.70 0.35 5.00 0

Posterior hypothalamic nucleus PH C57BL/6J 159649643 -1.50 0.35 5.20 0

Page 69: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 69 of 117

Posterior hypothalamic nucleus PH C57BL/6J 175374275 0.38 0.30 2.30 0

Posterior hypothalamic nucleus PH Calb2-IRES-Cre 267213793 -2.30 0.15 4.40 0

Posterior hypothalamic nucleus PH Cart-Tg1-Cre 176898557 0.38 0.50 3.90 0

Posterior hypothalamic nucleus PH Gad2-IRES-Cre 302086846 -2.30 0.15 4.40 0

Posterior hypothalamic nucleus PH Grm2-Cre_MR90 182182936 -2.35 0.13 5.10 0

Posterior hypothalamic nucleus PH Htr2a-Cre_KM207

293255030 -2.70 0.13 5.20 0

Posterior hypothalamic nucleus PH Oxtr-Cre_ON66 278260569 -2.30 0.15 4.40 0

Posterior hypothalamic nucleus PH Ppp1r17-Cre_NL146

268204599 -2.30 0.15 4.40 0

Posterior hypothalamic nucleus PH Ppp1r17-Cre_NL146

268208632 -2.30 0.25 3.90 0

Posterior hypothalamic nucleus PH Sim1-Cre 164986046 -2.30 0.25 4.37 0

Posterior limiting nucleus of the thalamus

POL Grm2-Cre_MR90 166267651 -3.16 1.60 2.89 0

Posterior limiting nucleus of the thalamus

POL Pdzk1ip1-Cre_KD31

170947610 -3.16 1.60 2.85 0

Posterior parietal association areas PTLp A930038C07Rik-Tg1-Cre

168165712 -2.54 1.75 0.20, 0.55

0

Posterior parietal association areas PTLp A930038C07Rik-Tg1-Cre

292792724 -2.46 2.75 0.35, 0.75

0

Posterior parietal association areas PTLp C57BL/6J 100148503 -2.54 1.75 0.20 0

Posterior parietal association areas PTLp C57BL/6J 112229103 -2.54 1.20 0.40 0

Posterior parietal association areas PTLp C57BL/6J 126861679 -2.54 1.75 0.55, 0.20

0

Posterior parietal association areas PTLp C57BL/6J 277714322 -3.28 2.50 0.50 0

Posterior parietal association areas PTLp Cux2-IRES-Cre 184167484 -2.54 1.75 0.20 0

Page 70: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 70 of 117

Posterior parietal association areas PTLp Cux2-IRES-Cre 286301303 -2.46 2.75 0.35 0

Posterior parietal association areas PTLp Cux2-IRES-Cre 294434867 -2.54 1.75 0.20, 0.55

0

Posterior parietal association areas PTLp Efr3a-Cre_NO108

267761438 -2.54 1.75 0.20, 0.55

0

Posterior parietal association areas PTLp Efr3a-Cre_NO108

286773358 -3.28 2.50 0.25, 0.75

0

Posterior parietal association areas PTLp Efr3a-Cre_NO108

309515141 -3.16 1.55 0.17 0

Posterior parietal association areas PTLp Etv1-CreERT2 182896517 -2.54 1.75 0.55, 0.20

0

Posterior parietal association areas PTLp Gpr26-Cre_KO250

267657327 -2.54 1.75 0.20, 0.55

0

Posterior parietal association areas PTLp Ntsr1-Cre_GN220

156671933 -2.54 1.75 0.55, 0.20

0

Posterior parietal association areas PTLp Rbp4-Cre_KL100 272929308 -2.46 2.75 0.35, 0.75

0

Posterior parietal association areas PTLp Rorb-IRES2-Cre 287225041 -2.54 1.75 0.20, 0.55

0

Posterior parietal association areas PTLp Scnn1a-Tg3-Cre 184073678 -2.46 3.28 0.21, 0.65

30

Posterior parietal association areas PTLp Scnn1a-Tg3-Cre 268038969 -2.54 1.75 0.20, 0.55

0

Posterior parietal association areas PTLp Sim1-Cre_KJ18 293821389 -2.54 1.75 0.20, 0.55

0

Posterior parietal association areas PTLp Sim1-Cre_KJ18 297712045 -2.46 2.75 0.35, 0.75

0

Posterior parietal association areas PTLp Sst-IRES-Cre 288264047 -2.54 1.75 0.20, 0.55

0

Posterior parietal association areas PTLp Syt6-Cre_KI148 157769139 -2.54 1.75 0.20, 0.55

0

Page 71: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 71 of 117

Posterior parietal association areas PTLp Syt6-Cre_KI148 299820770 -2.46 2.75 0.35, 0.75

0

Posterior parietal association areas PTLp Tlx3-Cre_PL56 294533406 -2.54 1.75 0.20, 0.55

0

Posterior parietal association areas PTLp Tlx3-Cre_PL56 297233422 -3.16 1.55 0.17, 0.58

0

Posterior parietal association areas PTLp Tlx3-Cre_PL56 303616127 -2.46 2.75 0.35, 0.75

0

Posterior parietal association areas PTLp Trib2-2A-CreERT2

287601808 -2.54 1.75 0.20, 0.55

0

Posterior pretectal nucleus PPT Pdzk1ip1-Cre_KD31

264097661 -2.50 0.75 2.40 0

Posterolateral visual area VISpl C57BL/6J 272916202 -4.60 3.80 0.45 30

Posterolateral visual area VISpl Rbp4-Cre_KL100 286417464 -4.60 3.80 0.45 30

Posterolateral visual area VISpl Scnn1a-Tg3-Cre 257667118 -4.60 3.80 0.45 30

posteromedial visual area VISpm A930038C07Rik-Tg1-Cre

286836394 -4.48 1.60 0.31 0

posteromedial visual area VISpm Nr5a1-Cre 177781745 -4.48 1.60 0.31 0

posteromedial visual area VISpm Ntsr1-Cre_GN220

159554010 -4.48 1.60 0.31 0

posteromedial visual area VISpm Ntsr1-Cre_GN220

297629282 -4.84 2.50 0.75 0

posteromedial visual area VISpm Oxtr-Cre_ON66 294312537 -4.84 2.50 0.31 0

posteromedial visual area VISpm Rbp4-Cre_KL100 168164230 -4.48 1.60 0.31 0

posteromedial visual area VISpm Rbp4-Cre_KL100 272930013 -4.84 2.50 0.31 0

posteromedial visual area VISpm Scnn1a-Tg3-Cre 184074388 -4.84 2.50 0.31 0

posteromedial visual area VISpm Scnn1a-Tg3-Cre 268040381 -4.48 1.60 0.31 0

posteromedial visual area VISpm Syt6-Cre_KI148 267032286 -4.84 2.50 0.75 0

Page 72: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 72 of 117

Postpiriform transition area TR C57BL/6J 126653015 -2.92 3.55 4.10 0

Postsubiculum POST C57BL/6J 126115436 -4.48 2.40 1.80 0

Postsubiculum POST C57BL/6J 127711098 -4.60 2.30 1.63 0

Postsubiculum POST Gad2-IRES-Cre 302217570 -4.16 2.25 2.27 0

Postsubiculum POST Htr2a-Cre_KM207

304694156 -4.04 2.00 1.50 0

Postsubiculum POST Oxtr-Cre_ON66 300623424 -4.04 2.00 1.50 0

Postsubiculum POST Scnn1a-Tg3-Cre 113934579 -4.04 2.00 1.50 0

Postsubiculum POST Scnn1a-Tg3-Cre 156314054 -4.60 2.30 1.63 0

Postsubiculum POST Slc17a6-IRES-Cre

167654019 -4.60 2.30 1.67 0

Prelimbic area PL A930038C07Rik-Tg1-Cre

292374777 2.10 0.06, 0.33 1.50 0

Prelimbic area PL C57BL/6J 157711748 2.10 0.25 1.50 0

Prelimbic area PL Cux2-IRES-Cre 278433737 2.10 0.06, 0.33 1.50 0

Prelimbic area PL Cux2-IRES-Cre 294396492 2.10 0.06, 0.33 1.50 0

Prelimbic area PL Cux2-IRES-Cre 294434161 1.10 0.25 1.30 0

Prelimbic area PL Glt25d2-Cre_NF107

305618479 2.10 0.06, 0.33 1.50 0

Prelimbic area PL Grp-Cre_KH288 266582782 2.10 0.06, 0.33 1.50 0

Prelimbic area PL Grp-Cre_KH288 292477301 2.68 0.05, 0.35 1.45 0

Prelimbic area PL Htr2a-Cre_KM207

266816894 2.10 0.06, 0.33 1.50 0

Prelimbic area PL Ntsr1-Cre_GN220

161463521 2.10 0.06, 0.33 1.50 0

Prelimbic area PL Rbp4-Cre_KL100 263106036 2.10 0.06, 0.33 1.50 0

Page 73: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 73 of 117

Presubiculum PRE C57BL/6J 146984915 -3.80 2.40 2.85 0

Presubiculum PRE Grm2-Cre_MR90 287172689 -3.80 2.40 2.85 0

Presubiculum PRE Rbp4-Cre_KL100 287028480 -4.72 3.40 2.20, 2.60

0

Presubiculum PRE Satb2-Cre_MO23 178488859 -4.96 3.00 2.55 0

Presubiculum PRE Scnn1a-Tg3-Cre 287772112 -4.60 2.40 2.55 0

Presubiculum PRE Slc17a6-IRES-Cre

302084009 -4.60 2.40 2.55 0

Primary auditory area AUDp A930038C07Rik-Tg1-Cre

156395997 -2.46 4.25 0.81 0

Primary auditory area AUDp C57BL/6J 100149109 -2.46 4.25 0.81 0

Primary auditory area AUDp C57BL/6J 120491896 -2.54 4.20 1.25 0

Primary auditory area AUDp Calb2-IRES-Cre 168455487 -0.70 3.50 0.35, 0.75

30

Primary auditory area AUDp Chrna2-Cre_OE25

296047084 -2.46 4.35 0.90 0

Primary auditory area AUDp Cort-T2A-Cre 165975810 -2.46 4.25 0.81 0

Primary auditory area AUDp Crh-IRES-Cre (BL)

183105218 -2.46 4.35 0.85 0

Primary auditory area AUDp Cux2-IRES-Cre 184159706 -2.46 4.35 0.85 0

Primary auditory area AUDp Etv1-CreERT2 156493815 -2.46 4.25 0.81 0

Primary auditory area AUDp Gad2-IRES-Cre 182934777 -2.46 4.35 0.85 0

Primary auditory area AUDp Gng7-Cre_KH71 157954927 -0.70 3.50 0.35, 0.75

30

Primary auditory area AUDp Gpr26-Cre_KO250

181600380 -2.46 4.25 0.81 0

Primary auditory area AUDp Htr3a-Cre_NO152

305488671 -2.46 4.35 0.90 0

Page 74: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 74 of 117

Primary auditory area AUDp Nos1-CreERT2 267930268 -2.46 4.35 0.90 0

Primary auditory area AUDp Ntsr1-Cre_GN220

266963362 -2.46 4.35 0.90 0

Primary auditory area AUDp Rbp4-Cre_KL100 182090318 -2.46 4.35 0.85 0

Primary auditory area AUDp Rorb-IRES2-Cre 287223629 -2.46 4.35 0.90 0

Primary auditory area AUDp Scnn1a-Tg3-Cre 166268376 -2.46 4.25 0.81 0

Primary auditory area AUDp Sim1-Cre_KJ18 293820681 -2.46 4.35 0.90 0

Primary auditory area AUDp Sst-IRES-Cre 182886547 -2.46 4.35 0.85 0

Primary auditory area AUDp Syt6-Cre_KI148 124060405 -2.46 4.25 0.81 0

Primary auditory area AUDp Trib2-2A-CreERT2

182686935 -2.46 4.35 0.85 0

Primary auditory area AUDp Vip-IRES-Cre 182040934 -2.46 4.25 0.81 0

Primary motor area MOp A930038C07Rik-Tg1-Cre

156394513 1.34 1.50 0.35, 0.75

0

Primary motor area MOp A930038C07Rik-Tg1-Cre

287461719 0.62 1.50 0.35, 0.70

0

Primary motor area MOp A930038C07Rik-Tg1-Cre

292374068 2.10 2.25 0.35, 1.00

30

Primary motor area MOp C57BL/6J 100141220 0.62 1.50 0.35, 0.70

0

Primary motor area MOp C57BL/6J 100141273 -0.34 1.50 0.45 0

Primary motor area MOp C57BL/6J 100141563 0.14 1.75 0.45 0

Primary motor area MOp C57BL/6J 100141780 1.10 2.00 0.30, 0.75

20

Primary motor area MOp C57BL/6J 112670853 2.10 2.25 0.35, 1.00

30

Primary motor area MOp C57BL/6J 112935169 -0.34 1.65 0.45 0

Page 75: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 75 of 117

Primary motor area MOp C57BL/6J 127084296 0.62 1.50 0.35, 0.70

0

Primary motor area MOp C57BL/6J 141602484 1.34 1.50 0.35, 0.75

0

Primary motor area MOp C57BL/6J 180709942 1.94 2.50 1.15 0

Primary motor area MOp C57BL/6J 180719293 2.10 2.40 0.40, 1.00

30

Primary motor area MOp C57BL/6J 180720175 -0.82 1.05 0.65 0

Primary motor area MOp Calb2-IRES-Cre 168454779 1.34 1.50 0.35, 0.75

0

Primary motor area MOp Chrna2-Cre_OE25

267750528 1.34 1.50 0.35, 0.75

0

Primary motor area MOp Chrna2-Cre_OE25

298273313 0.62 1.50 0.35, 0.70

0

Primary motor area MOp Chrnb4-Cre_OL57

297987980 2.10 2.25 0.35, 1.00

30

Primary motor area MOp Cort-T2A-Cre 157826227 1.34 1.50 0.35, 0.75

0

Primary motor area MOp Crh-IRES-Cre (BL)

183103805 1.34 1.50 0.35, 0.75

0

Primary motor area MOp Cux2-IRES-Cre 168002073 1.34 1.50 0.35 0

Primary motor area MOp Cux2-IRES-Cre 182616478 -0.54 1.65 0.45 0

Primary motor area MOp Cux2-IRES-Cre 263781454 0.14 0.90 0.40 0

Primary motor area MOp Cux2-IRES-Cre 266645328 2.10 2.25 0.35 30

Primary motor area MOp Cux2-CreERT2 310194040 1.70 1.85 2.83 0

Primary motor area MOp Efr3a-Cre_NO108

278258780 2.10 2.25 0.35, 1.00

30

Primary motor area MOp Efr3a-Cre_NO108

288169135 0.62 1.50 0.35, 0.70

0

Page 76: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 76 of 117

Primary motor area MOp Erbb4-2A-CreERT2

127908879 1.34 1.50 0.35, 0.75

0

Primary motor area MOp Esr1-2A-Cre 264249312 -1.50 0.78 5.76 0

Primary motor area MOp Etv1-CreERT2 167569313 1.34 1.50 0.35, 0.75

0

Primary motor area MOp Gad2-IRES-Cre 167440619 1.34 1.50 0.35, 0.75

0

Primary motor area MOp Gpr26-Cre_KO250

181598954 1.34 1.50 0.35, 0.75

0

Primary motor area MOp Gpr26-Cre_KO250

301267162 2.10 2.25 0.35, 1.00

30

Primary motor area MOp Grp-Cre_KH288 265289624 0.26 0.27 1.25 0

Primary motor area MOp Htr2a-Cre_KM207

183617432 1.34 1.50 0.35, 0.75

0

Primary motor area MOp Htr2a-Cre_KM207

258915564 2.10 2.25 0.35, 1.00

30

Primary motor area MOp Htr3a-Cre_NO152

305487964 1.34 1.50 0.35, 0.75

0

Primary motor area MOp Nr5a1-Cre 265929196 1.34 1.50 0.35, 0.75

0

Primary motor area MOp Ntsr1-Cre_GN220

120584036 1.34 1.50 0.35, 0.75

0

Primary motor area MOp Ntsr1-Cre_GN220

157909001 -0.34 1.65 0.45 0

Primary motor area MOp Ntsr1-Cre_GN220

159372889 2.10 2.25 0.35, 1.00

30

Primary motor area MOp Plxnd1-Cre 297669605 1.34 1.50 0.35, 0.75

0

Primary motor area MOp Pvalb-IRES-Cre 158138440 1.34 1.50 0.35, 0.75

0

Primary motor area MOp Rasgrf2-2A-dCre 298718072 1.34 1.50 0.35 0

Page 77: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 77 of 117

Primary motor area MOp Rbp4-Cre_KL100 120814821 1.34 1.50 0.35, 0.75

0

Primary motor area MOp Rbp4-Cre_KL100 166082128 2.10 2.25 0.35, 1.00

30

Primary motor area MOp Rbp4-Cre_KL100 166082842 -0.34 1.65 0.45 0

Primary motor area MOp Rbp4-Cre_KL100 182803137 -0.34 1.65 0.45 0

Primary motor area MOp Sim1-Cre_KJ18 287807030 1.34 1.50 0.35, 0.75

0

Primary motor area MOp Sim1-Cre_KJ18 287807743 1.34 1.50 0.35, 0.75

0

Primary motor area MOp Sim1-Cre_KJ18 297711339 0.62 1.50 0.35, 0.70

0

Primary motor area MOp Sim1-Cre_KJ18 297946935 2.10 2.25 0.35, 1.00

30

Primary motor area MOp Sst-IRES-Cre 277800995 1.34 1.50 0.35, 0.75

0

Primary motor area MOp Syt6-Cre_KI148 122642490 1.34 1.50 0.35, 0.75

0

Primary motor area MOp Syt6-Cre_KI148 168229113 0.62 1.50 0.35, 0.70

0

Primary motor area MOp Tac1-IRES2-Cre 181259279 1.34 1.50 0.35, 0.75

0

Primary motor area MOp Tlx3-Cre_PL56 288169842 1.34 1.50 0.35, 0.75

0

Primary motor area MOp Trib2-2A-CreERT2

266176167 1.34 1.50 0.35, 0.75

0

Primary motor area MOp Vip-IRES-Cre 179904912 1.34 1.50 0.35, 0.75

0

Primary somatosensory area SSp Nr5a1-Cre 277851379 -2.46 3.28 0.21, 0.65

30

Page 78: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 78 of 117

Primary somatosensory area SSp Nr5a1-Cre 293548317 -2.46 2.75 0.35, 0.75

0

Primary somatosensory area, barrel field

SSp-bfd A930038C07Rik-Tg1-Cre

171276330 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd A930038C07Rik-Tg1-Cre

177907797 -1.82 3.00 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd A930038C07Rik-Tg1-Cre

182467026 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd A930038C07Rik-Tg1-Cre

298326521 -0.22 3.88, 3.38 1.66 0

Primary somatosensory area, barrel field

SSp-bfd C57BL/6J 100141473 -2.54 3.50 0.45 30

Primary somatosensory area, barrel field

SSp-bfd C57BL/6J 112162251 -0.58 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd C57BL/6J 112373124 0.26 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd C57BL/6J 112882565 -2.46 3.75 0.65 0

Primary somatosensory area, barrel field

SSp-bfd C57BL/6J 112951804 -1.70 3.88, 3.38 1.25 0

Primary somatosensory area, barrel field

SSp-bfd C57BL/6J 126908007 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd C57BL/6J 127866392 -1.70 4.00 0.65 0

Primary somatosensory area, barrel field

SSp-bfd Calb2-IRES-Cre 168513750 -2.46 4.25 0.81 0

Primary somatosensory area, barrel field

SSp-bfd Cart-Tg1-Cre 159602992 -1.46 3.55 3.70 0

Primary somatosensory area, barrel field

SSp-bfd Chrna2-Cre_OE25

267749821 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Chrna2-Cre_OE25

293889922 -1.82 3.20 0.35, 0.75

30

Page 79: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 79 of 117

Primary somatosensory area, barrel field

SSp-bfd Cort-T2A-Cre 167374643 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Crh-IRES-Cre (BL)

266913240 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Cux2-IRES-Cre 168003640 -0.70 3.50 0.35 30

Primary somatosensory area, barrel field

SSp-bfd Cux2-IRES-Cre 266486371 -1.82 3.20 0.35 30

Primary somatosensory area, barrel field

SSp-bfd Drd3-Cre_KI196 293728197 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Drd3-Cre_KI196 297671018 -1.82 3.20 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Drd3-Cre_KI196 309427991 0.26 3.50 0.35 30

Primary somatosensory area, barrel field

SSp-bfd Drd3-Cre_KI196 309514434 -0.70 3.50 1.70 0

Primary somatosensory area, barrel field

SSp-bfd Efr3a-Cre_NO108

267660272 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Efr3a-Cre_NO108

286648997 -1.82 3.20 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Efr3a-Cre_NO108

292318449 0.26 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Erbb4-2A-CreERT2

127993375 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Etv1-CreERT2 286772650 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Gad2-IRES-Cre 167441329 -0.70 3.50 0.35, 0.75

0

Primary somatosensory area, barrel field

SSp-bfd Gng7-Cre_KH71 158017916 -4.48 2.70 0.35 0

Primary somatosensory area, barrel field

SSp-bfd Gpr26-Cre_KO250

175819113 -1.82 3.00 0.35, 0.75

30

Page 80: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 80 of 117

Primary somatosensory area, barrel field

SSp-bfd Gpr26-Cre_KO250

181599674 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Htr3a-Cre_NO152

305487234 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Nos1-CreERT2 182043055 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Nr5a1-Cre 176881134 -1.82 3.00 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Nr5a1-Cre 177322838 -0.70 3.88, 3.38 1.66 0

Primary somatosensory area, barrel field

SSp-bfd Ntsr1-Cre_GN220

159321097 -1.82 3.00 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Ntsr1-Cre_GN220

159651770 0.26 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Ntsr1-Cre_GN220

181180790 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Ntsr1-Cre_GN220

287037604 -0.34 3.50 2.95 0

Primary somatosensory area, barrel field

SSp-bfd Ntsr1-Cre_GN220

297628576 -2.46 2.75 0.35, 0.75

0

Primary somatosensory area, barrel field

SSp-bfd Ntsr1-Cre_GN220

303617548 -0.22 3.38, 3.88 1.66 0

Primary somatosensory area, barrel field

SSp-bfd Penk-IRES2-Cre 306268688 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Plxnd1-Cre 297668898 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Pvalb-IRES-Cre 158139151 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Pvalb-IRES-Cre 176496282 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Rasgrf2-2A-dCre 298718778 -0.70 3.50 0.35 30

Page 81: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 81 of 117

Primary somatosensory area, barrel field

SSp-bfd Rbp4-Cre_KL100 120875816 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Rbp4-Cre_KL100 120916102 -2.46 4.25 0.81 0

Primary somatosensory area, barrel field

SSp-bfd Rbp4-Cre_KL100 249327301 0.26 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Rbp4-Cre_KL100 272735030 -1.82 3.20 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Rbp4-Cre_KL100 298179622 -2.46 4.25 0.81 0

Primary somatosensory area, barrel field

SSp-bfd Rbp4-Cre_KL100 303785454 0.26 3.50 0.35 30

Primary somatosensory area, barrel field

SSp-bfd Rorb-IRES2-Cre 287174103 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Rorb-IRES2-Cre 301583889 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Scnn1a-Tg3-Cre 159888336 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Scnn1a-Tg3-Cre 181818339 -0.70 3.88, 3.38 1.66 0

Primary somatosensory area, barrel field

SSp-bfd Scnn1a-Tg3-Cre 181819064 0.26 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Scnn1a-Tg3-Cre 183374804 -1.82 3.20 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Scnn1a-Tg3-Cre 257666283 -0.22 3.88, 3.38 1.66 0

Primary somatosensory area, barrel field

SSp-bfd Sim1-Cre_KJ18 297710633 -1.82 3.20 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Sim1-Cre_KJ18 297713365 -0.70 4.00, 3.50 1.70 0

Primary somatosensory area, barrel field

SSp-bfd Sim1-Cre_KJ18 297948420 0.26 3.50 0.35, 0.75

30

Page 82: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 82 of 117

Primary somatosensory area, barrel field

SSp-bfd Sim1-Cre_KJ18 297985755 -0.22 3.88, 3.38 1.66 0

Primary somatosensory area, barrel field

SSp-bfd Sim1-Cre_KJ18 298760261 -0.70 3.50 0.35, 0.75

0

Primary somatosensory area, barrel field

SSp-bfd Slc18a2-Cre_OZ14

263370720 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Slc18a2-Cre_OZ14

265820951 -1.82 3.20 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Slc18a2-Cre_OZ14

306959448 0.26 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Sst-IRES-Cre 277801701 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Syt6-Cre_KI148 123664417 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Syt6-Cre_KI148 159223769 -1.82 3.00 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Syt6-Cre_KI148 168096467 -0.70 3.88, 3.38 1.66 0

Primary somatosensory area, barrel field

SSp-bfd Syt6-Cre_KI148 168229820 0.26 3.50 0.35, 0.75

0

Primary somatosensory area, barrel field

SSp-bfd Syt6-Cre_KI148 178487444 -2.46 3.28 0.21, 0.65

30

Primary somatosensory area, barrel field

SSp-bfd Tac1-IRES2-Cre 181371331 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Tlx3-Cre_PL56 288170549 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Tlx3-Cre_PL56 288171256 -2.46 4.35 0.90 0

Primary somatosensory area, barrel field

SSp-bfd Trib2-2A-CreERT2

266172624 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, barrel field

SSp-bfd Vip-IRES-Cre 180075597 -0.70 3.50 0.35, 0.75

30

Page 83: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 83 of 117

Primary somatosensory area, lower limb SSp-ll A930038C07Rik-Tg1-Cre

166323186 -1.06 2.25 0.35, 0.75

0

Primary somatosensory area, lower limb SSp-ll A930038C07Rik-Tg1-Cre

166461193 -0.34 1.65 0.45 0

Primary somatosensory area, lower limb SSp-ll A930038C07Rik-Tg1-Cre

264629246 -1.34 2.25 0.35, 0.75

25

Primary somatosensory area, lower limb SSp-ll A930038C07Rik-Tg1-Cre

281459203 -1.34 1.50 0.35, 0.75

0

Primary somatosensory area, lower limb SSp-ll C57BL/6J 112229814 -0.58 2.25 0.35, 0.75

20

Primary somatosensory area, lower limb SSp-ll C57BL/6J 114292355 -0.82 1.40 0.45 0

Primary somatosensory area, lower limb SSp-ll C57BL/6J 126852363 -1.58 1.50 0.35, 0.75

0

Primary somatosensory area, lower limb SSp-ll C57BL/6J 148964212 -0.30 2.00 4.85 0

Primary somatosensory area, lower limb SSp-ll C57BL/6J 180718587 -0.58 1.90 0.70 0

Primary somatosensory area, lower limb SSp-ll Chrna2-Cre_OE25

292124765 -1.34 1.50 0.35, 0.75

0

Primary somatosensory area, lower limb SSp-ll Chrna2-Cre_OE25

292173552 -0.34 2.10 0.45 0

Primary somatosensory area, lower limb SSp-ll Cux2-IRES-Cre 266644610 -0.34 1.85 0.45 0

Primary somatosensory area, lower limb SSp-ll Cux2-IRES-Cre 286300594 0.38 2.50 0.40 15

Primary somatosensory area, lower limb SSp-ll Efr3a-Cre_NO108

278257366 -0.34 2.10 0.45 0

Primary somatosensory area, lower limb SSp-ll Gpr26-Cre_KO250

267658747 -1.34 2.25 0.35, 0.75

25

Primary somatosensory area, lower limb SSp-ll Htr2a-Cre_KM207

277957908 0.62 1.50 0.35, 0.70

0

Primary somatosensory area, lower limb SSp-ll Nr5a1-Cre 166566678 -1.06 2.25 0.35, 0.75

25

Page 84: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 84 of 117

Primary somatosensory area, lower limb SSp-ll Ntsr1-Cre_GN220

266964788 -0.34 1.90 0.45 0

Primary somatosensory area, lower limb SSp-ll Rasgrf2-2A-dCre 303713313 -1.34 1.50 0.35, 0.75

0

Primary somatosensory area, lower limb SSp-ll Rbp4-Cre_KL100 272698650 -0.34 2.00 0.45 0

Primary somatosensory area, lower limb SSp-ll Rorb-IRES2-Cre 287880102 -1.34 1.50 0.35, 0.75

0

Primary somatosensory area, lower limb SSp-ll Rorb-IRES2-Cre 293700454 -0.34 2.10 0.45 0

Primary somatosensory area, lower limb SSp-ll Scnn1a-Tg3-Cre 166326029 -1.06 2.25 0.35, 0.75

25

Primary somatosensory area, lower limb SSp-ll Scnn1a-Tg3-Cre 179640955 -0.34 1.65 0.45 0

Primary somatosensory area, lower limb SSp-ll Sim1-Cre_KJ18 297714071 -0.34 2.10 0.45 0

Primary somatosensory area, lower limb SSp-ll Slc18a2-Cre_OZ14

266643194 -0.34 1.85 0.45 0

Primary somatosensory area, lower limb SSp-ll Syt6-Cre_KI148 156786234 -0.34 1.65 0.45 0

Primary somatosensory area, lower limb SSp-ll Tlx3-Cre_PL56 296052839 -0.34 2.10 0.45 0

Primary somatosensory area, lower limb SSp-ll Trib2-2A-CreERT2

292620251 -1.34 1.50 0.35, 0.75

0

Primary somatosensory area, mouth SSp-m A930038C07Rik-Tg1-Cre

298796577 0.26 3.50 0.35, 0.75

30

Primary somatosensory area, mouth SSp-m C57BL/6J 112936582 0.74 3.25 0.35, 0.75

0

Primary somatosensory area, mouth SSp-m C57BL/6J 114290938 0.74 3.70 0.40, 0.80

60

Primary somatosensory area, mouth SSp-m C57BL/6J 157654817 1.10 3.30 1.15 0

Primary somatosensory area, mouth SSp-m Cux2-IRES-Cre 278317945 0.26 3.50 0.35 30

Primary somatosensory area, mouth SSp-m Cux2-IRES-Cre 294397199 1.10 3.25, 3.00 1.90, 2.35

0

Primary somatosensory area, mouth SSp-m Nr5a1-Cre 177782493 0.26 3.50 0.35, 0.75

30

Page 85: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 85 of 117

Primary somatosensory area, mouth SSp-m Rorb-IRES2-Cre 301581763 0.26 3.50 0.35, 0.75

30

Primary somatosensory area, mouth SSp-m Scnn1a-Tg3-Cre 277852088 1.10 3.25, 3.00 1.90, 2.35

0

Primary somatosensory area, trunk SSp-tr C57BL/6J 100141495 -1.06 1.50 0.45 0

Primary somatosensory area, trunk SSp-tr C57BL/6J 100142655 -1.82 3.00 0.35, 0.75

30

Primary somatosensory area, trunk SSp-tr C57BL/6J 112791318 -1.06 2.25 0.35, 0.75

25

Primary somatosensory area, trunk SSp-tr C57BL/6J 126907302 -2.46 3.28 0.21, 0.65

30

Primary somatosensory area, trunk SSp-tr Chrna2-Cre_OE25

278175580 -2.54 1.75 0.20, 0.55

0

Primary somatosensory area, trunk SSp-tr Cux2-IRES-Cre 178284661 -1.06 2.25 0.35 25

Primary somatosensory area, trunk SSp-tr Cux2-IRES-Cre 294435580 -1.82 3.00 0.35, 0.75

30

Primary somatosensory area, trunk SSp-tr Cux2-IRES-Cre 298830161 -1.34 2.25 0.35, 0.75

25

Primary somatosensory area, trunk SSp-tr Efr3a-Cre_NO108

277907462 -1.34 2.25 0.35, 0.75

25

Primary somatosensory area, trunk SSp-tr Gpr26-Cre_KO250

298404154 -1.34 1.50 0.35, 0.75

0

Primary somatosensory area, trunk SSp-tr Nr5a1-Cre 115956702 -1.82 3.00 0.35, 0.75

30

Primary somatosensory area, trunk SSp-tr Ntsr1-Cre_GN220

157768393 -1.06 2.25 0.35, 0.75

25

Primary somatosensory area, trunk SSp-tr Ntsr1-Cre_GN220

166533924 -2.46 3.28 0.21, 0.65

30

Primary somatosensory area, trunk SSp-tr Ntsr1-Cre_GN220

304641170 -1.34 1.50 0.35, 0.75

0

Page 86: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 86 of 117

Primary somatosensory area, trunk SSp-tr Rbp4-Cre_KL100 183171679 -1.82 3.00 0.35, 0.75

30

Primary somatosensory area, trunk SSp-tr Rbp4-Cre_KL100 297652799 -1.06 2.25 0.35 25

Primary somatosensory area, trunk SSp-tr Scnn1a-Tg3-Cre 166459070 -1.82 3.00 0.35, 0.75

30

Primary somatosensory area, trunk SSp-tr Sim1-Cre_KJ18 299784429 -1.34 1.50 0.35, 0.75

0

Primary somatosensory area, trunk SSp-tr Slc18a2-Cre_OZ14

263553163 -1.34 2.25 0.35, 0.75

25

Primary somatosensory area, trunk SSp-tr Sst-IRES-Cre 304335875 -1.82 2.65 4.25 0

Primary somatosensory area, trunk SSp-tr Syt6-Cre_KI148 177319236 -1.06 2.25 0.35, 0.75

25

Primary somatosensory area, trunk SSp-tr Tlx3-Cre_PL56 297654263 -1.82 3.20 0.35, 0.75

30

Primary somatosensory area, trunk SSp-tr Tlx3-Cre_PL56 298182842 -1.34 1.50 0.35, 0.75

0

Primary somatosensory area, unassigned

SSp-un C57BL/6J 272697944 1.90 2.40 1.25 0

Primary somatosensory area, unassigned

SSp-un Scnn1a-Tg3-Cre 299447873 1.10 3.25, 3.0 1.90, 2.35

0

Primary somatosensory area, upper limb

SSp-ul A930038C07Rik-Tg1-Cre

292792016 0.38 2.50 0.40, 0.75

15

Primary somatosensory area, upper limb

SSp-ul C57BL/6J 126909424 0.38 2.50 0.40, 0.75

15

Primary somatosensory area, upper limb

SSp-ul Chrna2-Cre_OE25

298325807 0.38 2.50 0.40, 0.75

15

Primary somatosensory area, upper limb

SSp-ul Cux2-IRES-Cre 298106713 0.38 2.50 0.40 15

Primary somatosensory area, upper limb

SSp-ul Drd3-Cre_KI196 309428697 0.38 2.50 0.40 15

Page 87: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 87 of 117

Primary somatosensory area, upper limb

SSp-ul Efr3a-Cre_NO108

298352336 0.38 2.50 0.4, 0.75

15

Primary somatosensory area, upper limb

SSp-ul Etv1-CreERT2 167570021 -0.70 3.50 0.35, 0.75

30

Primary somatosensory area, upper limb

SSp-ul Nr5a1-Cre 177893658 0.35 2.50 0.40, 0.75

15

Primary somatosensory area, upper limb

SSp-ul Ntsr1-Cre_GN220

159651060 0.62 1.50 0.35, 0.70

0

Primary somatosensory area, upper limb

SSp-ul Ntsr1-Cre_GN220

162017460 0.38 2.50 0.40, 0.75

15

Primary somatosensory area, upper limb

SSp-ul Rbp4-Cre_KL100 266249483 -1.34 2.25 0.35, 0.75

25

Primary somatosensory area, upper limb

SSp-ul Rbp4-Cre_KL100 286312782 0.38 2.50 0.40, 0.75

15

Primary somatosensory area, upper limb

SSp-ul Scnn1a-Tg3-Cre 181860173 0.38 2.50 0.40, 0.75

15

Primary somatosensory area, upper limb

SSp-ul Sim1-Cre_KJ18 297951732 0.38 2.50 0.40, 0.75

15

Primary somatosensory area, upper limb

SSp-ul Slc18a2-Cre_OZ14

306990880 0.38 2.50 0.4, 0.75

15

Primary somatosensory area, upper limb

SSp-ul Syt6-Cre_KI148 179641666 0.38 2.50 0.40, 0.75

15

Primary somatosensory area, upper limb

SSp-ul Tlx3-Cre_PL56 303614706 0.26 3.50 0.35, 0.75

30

Primary somatosensory area, upper limb

SSp-ul Tlx3-Cre_PL56 303615412 0.38 2.50 0.4, 0.75

15

Primary visual area VISp A930038C07Rik-Tg1-Cre

158255941 -4.48 2.70 0.35 0

Primary visual area VISp A930038C07Rik-Tg1-Cre

166324604 -3.80 2.50 0.35, 0.75

0

Primary visual area VISp A930038C07Rik-Tg1-Cre

283020912 -3.28 2.50 0.25, 0.75

0

Page 88: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 88 of 117

Primary visual area VISp A930038C07Rik-Tg1-Cre

292793967 -4.84 2.50 0.31 0

Primary visual area VISp A930038C07Rik-Tg1-Cre

298351630 -3.28 2.50 0.25, 0.75

0

Primary visual area VISp C57BL/6J 100141219 -3.80 2.50 0.35, 0.75

0

Primary visual area VISp C57BL/6J 100147853 -4.48 2.70 0.35 0

Primary visual area VISp C57BL/6J 113887162 -3.28 2.50 0.25, 0.75

0

Primary visual area VISp C57BL/6J 113887868 -4.84 2.50 0.31 0

Primary visual area VISp C57BL/6J 126862385 -4.48 1.60 0.31 0

Primary visual area VISp C57BL/6J 127138787 -4.60 3.60 0.45 30

Primary visual area VISp C57BL/6J 174361040 -4.36 1.65 0.38 0

Primary visual area VISp C57BL/6J 180296424 -4.60 3.45 0.80 0

Primary visual area VISp C57BL/6J 272782668 -4.48 1.62 0.31 0

Primary visual area VISp C57BL/6J 277616630 -3.28 2.50 0.50 0

Primary visual area VISp C57BL/6J 277712166 -3.28 2.50 0.50 0

Primary visual area VISp C57BL/6J 277713580 -3.28 2.50 0.50 0

Primary visual area VISp Calb2-IRES-Cre 168515938 -4.48 2.70 0.35 0

Primary visual area VISp Chrna2-Cre_OE25

278068196 -2.46 4.35 0.90 0

Primary visual area VISp Chrna2-Cre_OE25

292126180 -3.80 2.50 0.35, 0.75

0

Primary visual area VISp Chrna2-Cre_OE25

297597186 -3.28 2.50 0.25, 0.75

0

Primary visual area VISp Chrna2-Cre_OE25

299781566 -4.84 2.50 0.31 0

Primary visual area VISp Cort-T2A-Cre 167375352 -4.48 2.70 0.35 0

Page 89: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 89 of 117

Primary visual area VISp Crh-IRES-Cre (BL)

266836749 -4.48 2.70 0.35 0

Primary visual area VISp Cux2-IRES-Cre 183471884 -4.48 2.70 0.35 0

Primary visual area VISp Cux2-IRES-Cre 272821309 -3.28 2.50 0.25 0

Primary visual area VISp Cux2-IRES-Cre 286302294 -4.84 2.50 0.31 0

Primary visual area VISp Cux2-IRES-Cre 293472335 -3.28 2.50 0.25 0

Primary visual area VISp Cux2-IRES-Cre 298829455 -4.60 3.80 0.45 30

Primary visual area VISp Drd3-Cre_KI196 298759552 -4.84 2.50 0.75 0

Primary visual area VISp Efr3a-Cre_NO108

267704653 -4.48 2.70 0.35 0

Primary visual area VISp Efr3a-Cre_NO108

286835688 -3.40 3.60 0.45 0

Primary visual area VISp Efr3a-Cre_NO108

298350212 -3.80 2.50 0.35, 0.75

0

Primary visual area VISp Efr3a-Cre_NO108

294266031 -4.60 3.80 0.45 30

Primary visual area VISp Efr3a-Cre_NO108

309564818 -4.04 4.00 0.35 0

Primary visual area VISp Erbb4-2A-CreERT2

182184486 -4.48 2.70 0.35 0

Primary visual area VISp Etv1-CreERT2 156494530 -4.48 2.70 0.35 0

Primary visual area VISp Gad2-IRES-Cre 167511639 -4.48 2.70 0.35 0

Primary visual area VISp Gng7-Cre_KH71 157955639 -2.46 4.25 0.81 0

Primary visual area VISp Gpr26-Cre_KO250

181601101 -4.48 2.70 0.35 0

Primary visual area VISp Gpr26-Cre_KO250

301263519 -3.28 2.50 0.25, 0.75

0

Primary visual area VISp Htr3a-Cre_NO152

305489377 -4.48 2.70 0.35 0

Page 90: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 90 of 117

Primary visual area VISp Nos1-CreERT2 267931685 -4.48 2.70 0.35 0

Primary visual area VISp Nos1-CreERT2 293116943 -4.48 2.70 0.35 0

Primary visual area VISp Nr5a1-Cre 176882966 -3.40 3.50 0.45 0

Primary visual area VISp Nr5a1-Cre 176901480 -3.28 2.50 0.25, 0.75

0

Primary visual area VISp Nr5a1-Cre 177781006 -3.80 2.00 0.35, 0.75

0

Primary visual area VISp Nr5a1-Cre 266100645 -4.84 2.50 0.31 0

Primary visual area VISp Nr5a1-Cre 266177248 -4.04 4.00 0.35, 0.75

30

Primary visual area VISp Ntsr1-Cre_GN220

156545918 -4.48 2.70 0.35 0

Primary visual area VISp Ntsr1-Cre_GN220

159550125 -3.28 2.50 0.25, 0.75

0

Primary visual area VISp Ntsr1-Cre_GN220

181258571 -3.80 2.50 0.35, 0.75

0

Primary visual area VISp Ntsr1-Cre_GN220

297629988 -4.60 3.80 0.45 30

Primary visual area VISp Plxnd1-Cre 299859225 -4.48 2.70 0.35 0

Primary visual area VISp Pvalb-IRES-Cre 166562678 -4.48 2.70 0.35 0

Primary visual area VISp Rasgrf2-2A-dCre 298758133 -4.48 2.70 0.35 0

Primary visual area VISp Rbp4-Cre_KL100 121510421 -4.48 2.70 0.35 0

Primary visual area VISp Rbp4-Cre_KL100 183173527 -3.28 2.50 0.25, 0.75

0

Primary visual area VISp Rbp4-Cre_KL100 266250195 -3.80 2.50 0.35, 0.75

0

Primary visual area VISp Rbp4-Cre_KL100 294482052 -3.80 2.50 0.35 0

Primary visual area VISp Rorb-IRES2-Cre 287224335 -4.48 2.70 0.35 0

Page 91: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 91 of 117

Primary visual area VISp Rorb-IRES2-Cre 300929973 -3.28 2.50 0.25, 0.75

0

Primary visual area VISp Rorb-IRES2-Cre 301616660 -4.48 2.70 0.35 0

Primary visual area VISp Rorb-IRES2-Cre 301617370 -4.60 3.80 0.45 30

Primary visual area VISp Scnn1a-Tg3-Cre 166269819 -4.48 2.70 0.35 0

Primary visual area VISp Scnn1a-Tg3-Cre 166326736 -3.80 2.50 0.35, 0.75

0

Primary visual area VISp Scnn1a-Tg3-Cre 182089608 -3.28 2.50 0.25, 0.75

0

Primary visual area VISp Sst-IRES-Cre 288261928 -4.48 2.70 0.35 0

Primary visual area VISp Syt6-Cre_KI148 125435783 -4.48 2.70 0.35 0

Primary visual area VISp Syt6-Cre_KI148 156784823 -3.80 2.50 0.35, 0.75

0

Primary visual area VISp Syt6-Cre_KI148 159330030 -3.28 2.50 0.25, 0.75

0

Primary visual area VISp Syt6-Cre_KI148 168097187 -4.48 1.60 0.31 0

Primary visual area VISp Syt6-Cre_KI148 297671724 -4.84 2.50 0.75 0

Primary visual area VISp Syt6-Cre_KI148 299828473 -4.60 3.80 0.45 30

Primary visual area VISp Tlx3-Cre_PL56 288171964 -4.48 2.70 0.35 0

Primary visual area VISp Tlx3-Cre_PL56 296052133 -3.80 2.50 0.35, 0.75

0

Primary visual area VISp Tlx3-Cre_PL56 297592527 -3.28 2.50 0.25, 0.75

0

Primary visual area VISp Tlx3-Cre_PL56 297593235 -4.84 2.50 0.31 0

Primary visual area VISp Tlx3-Cre_PL56 297593942 -4.60 3.80 0.45 30

Primary visual area VISp Trib2-2A-CreERT2

268320515 -4.48 2.70 0.35 0

Primary visual area VISp Trib2-2A-CreERT2

308879859 -3.80 2.50 0.35, 0.75

0

Page 92: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 92 of 117

Primary visual area VISp Vip-IRES-Cre 182293273 -4.48 2.70 0.35 0

Primary visual area, layer 4 VISp4 Nr5a1-Cre 157767683 -4.48 2.70 0.35 0

Principal sensory nucleus of the trigeminal

PSV C57BL/6J 114755811 -5.20 1.95 3.35 0

Principal sensory nucleus of the trigeminal

PSV C57BL/6J 156979988 -4.04 2.25 4.65 0

Principal sensory nucleus of the trigeminal

PSV Gad2-IRES-Cre 303535867 -4.36 1.60 4.27 0

Principal sensory nucleus of the trigeminal

PSV Syt6-Cre_KI148 182465608 -4.36 1.60 4.27 0

Pyramus (VIII) PYR C57BL/6J 125831616 -7.32 0.50 1.63 0

Red nucleus RN C57BL/6J 113400134 -3.28 0.36 4.13 0

Red nucleus RN C57BL/6J 120811946 -3.08 1.25 4.15 0

Red Nucleus RN Rbp4-Cre_KL100 300624130 -3.28 0.60 3.65 0

Reticular nucleus of the thalamus RT C57BL/6J 117316260 -0.34 1.70 3.58 0

Reticular nucleus of the thalamus RT C57BL/6J 127468854 -0.70 1.80 3.95 0

Reticular nucleus of the thalamus RT Gad2-IRES-Cre 156252954 -0.70 1.53 3.48 0

Reticular nucleus of the thalamus RT Gad2-IRES-Cre 156254369 -1.22 2.00 3.09 0

Reticular nucleus of the thalamus RT Oxtr-Cre_ON66 301421253 -2.30 2.55 3.00 0

Reticular nucleus of the thalamus RT Pvalb-IRES-Cre 127085005 -0.70 1.53 3.48 0

Reticular nucleus of the thalamus RT Pvalb-IRES-Cre 127090378 -1.22 2.00 3.09 0

Reticular nucleus of the thalamus RT Pvalb-IRES-Cre 277958616 -0.70 1.80 3.95 0

Reticular nucleus of the thalamus RT Pvalb-IRES-Cre 299894738 -0.34 1.70 3.58 0

Reticular nucleus of the thalamus RT Slc32a1-IRES-Cre

171064488 -0.70 1.53 3.48 0

Reticular nucleus of the thalamus RT Slc32a1-IRES-Cre

171065200 -1.22 2.00 3.09 0

Page 93: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 93 of 117

Retrochiasmatic area RCH Lypd6-Cre_KL156

305092904 -0.34 0.20 5.60 0

Retrosplenial area RSP A930038C07Rik-Tg1-Cre

166271142 -2.06 0.17 0.63 0

Retrosplenial area RSP C57BL/6J 100148142 -2.06 0.17 0.63 0

Retrosplenial area RSP Chrna2-Cre_OE25

298275548 -3.28 1.06 1.17 0

Retrosplenial area RSP Cux2-IRES-Cre 272735744 -3.00 0.45 0.40 0

Retrosplenial area RSP Etv1-CreERT2 159097209 -2.06 0.17 0.63 0

Retrosplenial area RSP Scnn1a-Tg3-Cre 166269090 -2.06 0.17 0.63 0

Retrosplenial area, dorsal part RSPd A930038C07Rik-Tg1-Cre

166325321 -3.00 0.45 0.40 0

Retrosplenial area, dorsal part RSPd Adcyap1-2A-Cre 306491185 -1.70 0.42 2.45 0

Retrosplenial area, dorsal part RSPd C57BL/6J 112424813 -3.00 0.45 0.40 0

Retrosplenial area, dorsal part RSPd Chrnb4-Cre_OL57

298000880 -1.70 0.42 2.45 0

Retrosplenial area, dorsal part RSPd Efr3a-Cre_NO108

267661018 -2.06 0.17 0.63 0

Retrosplenial area, dorsal part RSPd Efr3a-Cre_NO108

278179794 -3.80 2.50 0.35, 0.75

0

Retrosplenial area, dorsal part RSPd Gpr26-Cre_KO250

267658040 -2.06 0.17 0.63 0

Retrosplenial area, dorsal part RSPd Gpr26-Cre_KO250

298404860 -3.80 2.50 0.35, 0.75

0

Retrosplenial area, dorsal part RSPd Gpr26-Cre_KO250

298720191 -3.00 0.45 0.40 0

Retrosplenial area, dorsal part RSPd Rbp4-Cre_KL100 166054929 -3.00 0.45 0.40 0

Retrosplenial area, dorsal part RSPd Scnn1a-Tg3-Cre 166458363 -3.00 0.45 0.40 0

Retrosplenial area, dorsal part RSPd Sst-IRES-Cre 288264753 -2.06 0.17 0.63 0

Page 94: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 94 of 117

Retrosplenial area, lateral agranular part RSPagl C57BL/6J 272916915 -3.16 1.20 0.55 0

Retrosplenial area, lateral agranular part RSPagl Chrna2-Cre_OE25

297627858 -4.48 1.60 0.31 0

Retrosplenial area, lateral agranular part RSPagl Cux2-IRES-Cre 294484177 -4.48 1.60 0.31 0

Retrosplenial area, lateral agranular part RSPagl Efr3a-Cre_NO108

288168426 -4.48 1.60 0.31 0

Retrosplenial area, ventral part RSPv A930038C07Rik-Tg1-Cre

292373346 -3.28 1.06 1.17 0

Retrosplenial area, ventral part RSPv C57BL/6J 100140949 -2.06 0.17 0.63 0

Retrosplenial area, ventral part RSPv C57BL/6J 100142354 -4.04 2.00 1.50 0

Retrosplenial area, ventral part RSPv C57BL/6J 112516334 -2.06 0.17 0.60 0

Retrosplenial area, ventral part RSPv C57BL/6J 112595376 -3.28 1.06 1.17 0

Retrosplenial area, ventral part RSPv Chrna2-Cre_OE25

292124058 -2.06 0.17 0.63 0

Retrosplenial area, ventral part RSPv Chrna2-Cre_OE25

292172100 -3.00 0.45 0.40 0

Retrosplenial area, ventral part RSPv Cux2-IRES-Cre 177907082 -2.06 0.17 0.63 0

Retrosplenial area, ventral part RSPv Cux2-IRES-Cre 182467736 -3.00 0.45 0.40 0

Retrosplenial area, ventral part RSPv Cux2-IRES-Cre 184168193 -2.06 0.17 0.63 0

Retrosplenial area, ventral part RSPv Drd3-Cre_KI196 304693450 -4.04 2.00 1.50 0

Retrosplenial area, ventral part RSPv Nos1-CreERT2 308027576 -2.06 0.17 0.63 0

Retrosplenial area, ventral part RSPv Rbp4-Cre_KL100 159832064 -2.06 0.17 0.63 0

Retrosplenial area, ventral part RSPv Rbp4-Cre_KL100 249396394 -3.28 1.06 1.17 0

Retrosplenial area, ventral part RSPv Rbp4-Cre_KL100 303784745 -3.28 1.06 1.17 0

Retrosplenial area, ventral part RSPv Scnn1a-Tg3-Cre 181860879 -3.28 1.06 1.17 0

Retrosplenial area, ventral part RSPv Syt6-Cre_KI148 157711043 -3.00 0.45 0.40 0

Retrosplenial area, ventral part RSPv Syt6-Cre_KI148 168363168 -3.28 1.06 1.17 0

Page 95: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 95 of 117

Retrosplenial area, ventral part RSPv Syt6-Cre_KI148 176497015 -2.06 0.17 0.63 0

Retrosplenial area, ventral part RSPv Trib2-2A-CreERT2

287601100 -2.06 0.17 0.63 0

Retrosplenial area, ventral part RSPv Trib2-2A-CreERT2

308721884 -2.06 0.17 0.63 0

Secondary motor area MOs A930038C07Rik-Tg1-Cre

166460484 2.10 0.75 0.35, 0.75

0

Secondary motor area MOs A930038C07Rik-Tg1-Cre

176433237 0.14 0.90 0.40, 0.80

0

Secondary motor area MOs A930038C07Rik-Tg1-Cre

292476595 3.70 1.50 0.40 0

Secondary motor area MOs C57BL/6J 100140756 3.08 1.50 0.40 0

Secondary motor area MOs C57BL/6J 100141454 2.10 0.75 0.35, 0.75

0

Secondary motor area MOs C57BL/6J 112952510 1.70 0.90 0.40, 0.80

0

Secondary motor area MOs C57BL/6J 141603190 1.00 0.75 0.30, 0.75

0

Secondary motor area MOs C57BL/6J 157710335 3.08 1.50 0.40 0

Secondary motor area MOs C57BL/6J 180916954 0.14 0.60 0.60 0

Secondary motor area MOs Chrna2-Cre_OE25

292172846 2.10 0.75 0.35, 0.75

0

Secondary motor area MOs Chrna2-Cre_OE25

292174974 0.14 0.90 0.40, 0.80

0

Secondary motor area MOs Chrna2-Cre_OE25

292210312 2.10 2.25 0.35, 1.00

30

Secondary motor area MOs Chrnb4-Cre_OL57

298000163 1.00 0.75 0.30, 0.75

0

Secondary motor area MOs Crh-IRES-Cre (BL)

183172820 0.26 0.27 0.60 0

Page 96: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 96 of 117

Secondary motor area MOs Cux2-IRES-Cre 182461051 2.10 0.75 0.35 0

Secondary motor area MOs Cux2-IRES-Cre 272822110 1.00 0.75 0.30 0

Secondary motor area MOs Cux2-IRES-Cre 286299886 3.70 1.50 0.40 0

Secondary motor area MOs Efr3a-Cre_NO108

267659565 1.34 1.50 0.35, 0.75

0

Secondary motor area MOs Efr3a-Cre_NO108

278181912 2.10 0.75 0.35, 0.75

0

Secondary motor area MOs Efr3a-Cre_NO108

278258073 0.14 0.90 0.40, 0.80

0

Secondary motor area MOs Efr3a-Cre_NO108

287995889 1.00 0.75 0.30, 0.75

0

Secondary motor area MOs Etv1-CreERT2 156492394 1.34 1.50 0.35, 0.75

0

Secondary motor area MOs Glt25d2-Cre_NF107

313327735 2.80 1.25 1.30 0

Secondary motor area MOs Gpr26-Cre_KO250

258316155 0.26 0.27 0.60 0

Secondary motor area MOs Gpr26-Cre_KO250

298601161 2.10 0.80 0.35, 0.75

0

Secondary motor area MOs Grm2-Cre_MR90 182795499 3.08 1.50 0.40 0

Secondary motor area MOs Grm2-Cre_MR90 182814071 2.10 0.75 0.35, 0.75

0

Secondary motor area MOs Grm2-Cre_MR90 300235349 3.10 1.50 0.40 0

Secondary motor area MOs Grp-Cre_KH288 265292679 0.14 0.90 0.40, 0.80

0

Secondary motor area MOs Grp-Cre_KH288 266503540 1.00 0.75 0.30, 0.75

0

Secondary motor area MOs Grp-Cre_KH288 292034715 2.95 1.50 0.40 0

Secondary motor area MOs Htr2a-Cre_KM207

277957202 1.00 0.75 0.30, 0.75

0

Page 97: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 97 of 117

Secondary motor area MOs Htr2a-Cre_KM207

293433996 3.70 1.50 0.40 0

Secondary motor area MOs Nos1-CreERT2 267813224 1.34 1.50 0.35, 0.75

0

Secondary motor area MOs Nos1-CreERT2 267930978 0.26 0.27 0.60 0

Secondary motor area MOs Nr5a1-Cre 167791990 2.10 0.75 0.35, 0.75

0

Secondary motor area MOs Ntsr1-Cre_GN220

158139883 0.14 0.90 0.40, 0.80

0

Secondary motor area MOs Ntsr1-Cre_GN220

159373612 0.14 0.90 0.40, 0.80

0

Secondary motor area MOs Ntsr1-Cre_GN220

159551564 -0.34 4.00, 3.75 3.00, 3.25

0

Secondary motor area MOs Rasgrf2-2A-dCre 298758841 0.26 0.27 0.60 0

Secondary motor area MOs Rbp4-Cre_KL100 166055636 2.10 0.75 0.35, 0.75

0

Secondary motor area MOs Rbp4-Cre_KL100 168162771 1.00 0.75 0.30, 0.75

0

Secondary motor area MOs Rbp4-Cre_KL100 182793477 0.14 0.90 0.40, 0.80

0

Secondary motor area MOs Rbp4-Cre_KL100 263242463 3.08 1.50 0.40 0

Secondary motor area MOs Sim1-Cre_KJ18 293827470 2.10 0.80 0.35, 0.75

0

Secondary motor area MOs Sim1-Cre_KJ18 297854981 0.14 0.90 0.40, 0.80

0

Secondary motor area MOs Sim1-Cre_KJ18 297947641 1.00 0.75 0.30, 0.75

0

Secondary motor area MOs Syt6-Cre_KI148 159330754 1.00 0.75 0.30, 0.75

0

Secondary motor area MOs Syt6-Cre_KI148 177319974 0.14 0.90 0.40, 0.80

0

Page 98: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 98 of 117

Secondary motor area MOs Syt6-Cre_KI148 177459319 2.10 0.75 0.35, 0.75

0

Secondary motor area MOs Syt6-Cre_KI148 177890246 3.08 1.50 0.40 0

Secondary motor area MOs Syt6-Cre_KI148 287633753 2.10 2.25 0.35, 1.00

30

Secondary motor area MOs Tlx3-Cre_PL56 293431869 0.26 0.27 0.60 0

Secondary motor area MOs Tlx3-Cre_PL56 293432575 0.26 0.25 1.25 0

Secondary motor area MOs Tlx3-Cre_PL56 294525944 0.14 0.90 0.40, 0.80

0

Secondary motor area MOs Tlx3-Cre_PL56 294532700 2.10 0.80 0.35, 0.75

0

Secondary motor area MOs Tlx3-Cre_PL56 297892130 1.00 0.75 0.30, 0.75

0

Secondary motor area MOs Vip-IRES-Cre 182935487 0.26 0.27 0.80 0

Septofimbrial nucleus SF Calb2-IRES-Cre 287950390 -0.10 0.10 2.30 0

Septofimbrial nucleus SF Syt6-Cre_KI148 182341627 0.02 0.40 3.08 0

Simple lobule SIM C57BL/6J 112460257 -5.88 2.25 2.19 0

Simple lobule SIM C57BL/6J 113936696 -5.68 2.25 0.42, 1.05

0

Simple lobule SIM Gabra6-IRES-Cre

159945113 -6.48 2.50 0.57 0

Simple lobule SIM Gad2-IRES-Cre 287539649 -5.88 2.25 2.19 0

Simple lobule SIM Gad2-IRES-Cre 302079862 -4.60 2.40 2.55 0

Simple lobule SIM Nos1-CreERT2 300622004 -5.68 2.25 0.42, 1.05

0

Simple lobule SIM Pcp2-Cre_GN135

168299316 -5.68 2.25 0.42, 1.05

0

Simple lobule SIM Ppp1r17-Cre_NL146

267811103 -6.48 2.50 0.57 0

Page 99: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 99 of 117

Simple lobule SIM Ppp1r17-Cre_NL146

268165349 -5.68 2.25 0.42, 1.05

0

Simple lobule SIM Slc17a7-IRES2-Cre

267106046 -5.68 2.25 0.42, 1.05

0

Spinal nucleus of the trigeminal, caudal part

SPVC C57BL/6J 114402050 0.20 calamus

(-7.00 bregma)

1.25 0.15 0

Spinal nucleus of the trigeminal, caudal part

SPVC C57BL/6J 122640358 -0.32 calamus

(-7.64 bregma)

0.80 0.28 0

Spinal nucleus of the trigeminal, caudal part

SPVC C57BL/6J 126352744 -6.96 1.80 3.40 0

Spinal nucleus of the trigeminal, caudal part

SPVC C57BL/6J 146856593 0.30 calamus

(-6.90 bregma)

1.20 0.15 0

Spinal nucleus of the trigeminal, caudal part

SPVC C57BL/6J 147215105 -0.44 calamus

(-7.76 bregma)

1.75 0.61 0

Spinal nucleus of the trigeminal, caudal part

SPVC C57BL/6J 147790181 0.00 calamus

(-7.32 bregma)

1.00 1.36 0

Spinal nucleus of the trigeminal, caudal part

SPVC Cck-IRES-Cre 287460307 -0.44 calamus

(-7.76 Bregma)

1.75 0.61 0

Spinal nucleus of the trigeminal, caudal part

SPVC Slc32a1-IRES-Cre

305319461 -0.44 calamus

(-7.76 Bregma)

1.75 0.61 0

Page 100: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 100 of 117

Spinal nucleus of the trigeminal, caudal part

SPVC Slc6a5-Cre_KF109

126908712 -7.56 1.25 3.06 0

Spinal nucleus of the trigeminal, caudal part

SPVC Syt6-Cre_KI148 264096244 -0.44 calamus

(-7.76 bregma)

1.75 0.61 0

Spinal nucleus of the trigeminal, caudal part

SPVC Th-Cre 311846681 -0.44 1.75 0.61 0

Spinal nucleus of the trigeminal, interpolar part

SPVI C57BL/6J 272738620 -6.84 1.80 3.40 0

Spinal nucleus of the trigeminal, interpolar part

SPVI Slc6a5-Cre_KF109

160150861 -6.00 1.83 3.95 0

Spinal nucleus of the trigeminal, interpolar part

SPVI Slc6a5-Cre_KF109

160151570 -6.96 1.80 3.40 0

Spinal nucleus of the trigeminal, oral part

SPVO C57BL/6J 112826458 -6.00 1.83 3.95 0

Spinal vestibular nucleus SPIV C57BL/6J 126351299 -6.00 1.40 3.20 0

Spinal vestibular nucleus SPIV C57BL/6J 128056535 -6.48 1.25 3.25 0

Spinal vestibular nucleus SPIV C57BL/6J 129567943 -5.68 1.13 3.00 0

Striatum dorsal region CP Chat-IRES-Cre 307692311 -1.34 2.80 1.84 0

Striatum dorsal region CP Chat-IRES-Cre 307909888 -0.70 2.70 2.39 0

Striatum dorsal region CP Chat-IRES-Cre 307910595 0.14 1.75 2.53 0

Striatum dorsal region CP Efr3a-Cre_NO108

301180385 -1.34 2.80 1.84 0

Striatum dorsal region CP Gad2-IRES-Cre 303478748 -1.06 3.00 3.90 0

Striatum dorsal region CP Ntrk1-IRES-Cre 308395312 0.14 1.75 2.53 0

Striatum dorsal region CP Slc18a2-Cre_OZ14

301620241 0.14 1.75 2.53 0

Subiculum SUB C57BL/6J 114008926 -3.52 2.50 1.35 0

Page 101: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 101 of 117

Subiculum, dorsal part SUBd C57BL/6J 127795906 -3.52 2.50 1.35 0

Subiculum, dorsal part SUBd C57BL/6J 157063781 -2.55 0.13 5.30 0

Subiculum, dorsal part SUBd Drd1a-Cre 113368898 -2.85 0.70 1.85 0

Subiculum, dorsal part SUBd Slc17a6-IRES-Cre

159374329 -4.04 2.00 1.50 0

Subiculum, dorsal part SUBd Slc32a1-IRES-Cre

264077561 -2.70 0.56 1.92 0

Subiculum, dorsal part SUBd Syt17-Cre_NO14 293009970 -2.92 1.85 1.95 0

Subiculum, ventral part SUBv A930038C07Rik-Tg1-Cre

298831574 -4.72 3.40 2.2, 2.6

0

Subiculum, ventral part SUBv C57BL/6J 122641784 -2.54 4.25 3.32 25

Subiculum, ventral part SUBv C57BL/6J 127222723 -4.04 3.35 2.60 0

Subiculum, ventral part SUBv C57BL/6J 152994878 -4.04 3.50 2.60 0

Subiculum, ventral part SUBv Cux2-IRES-Cre 298795868 -4.72 3.40 2.20 0

Subiculum, ventral part SUBv Drd3-Cre_KI196 293701770 -4.16 3.80 3.00 0

Subiculum, ventral part SUBv Gad2-IRES-Cre 167513067 -2.70 0.56 1.92 0

Subiculum, ventral part SUBv Grik4-Cre 264945172 -4.00 3.40 2.60 0

Subiculum, ventral part SUBv Rbp4-Cre_KL100 299446445 -4.72 3.40 2.2, 2.6

0

Subiculum, ventral part SUBv Scnn1a-Tg3-Cre 268041088 -4.04 3.80 1.90 0

Subiculum, ventral part SUBv Syt17-Cre_NO14 286610216 -3.08 3.00 3.60 0

Subiculum, ventral part SUBv Tac1-IRES2-Cre 294314037 -4.72 3.40 2.20, 2.60

0

Sublaterodorsal nucleus SLD Crh-IRES-Cre (BL)

277853501 -5.52 0.88 2.71 0

Sublaterodorsal nucleus SLD Crh-IRES-Cre (BL)

278180500 -4.22 0.25 4.40 0

Submedial nucleus of the thalamus SMT Vipr2-Cre_KE2 268163228 -1.34 0.32 4.05 0

Page 102: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 102 of 117

Subparafascicular area SPA Calb2-IRES-Cre 184158996 -2.18 1.23 3.71 20

Subparafascicular nucleus, magnocellular part

SPFm C57BL/6J 273025872 -1.22 0.30 4.15 0

Subparafascicular nucleus, magnocellular part

SPFm Pdzk1ip1-Cre_KD31

159258618 -2.30 0.25 3.90 0

Subparafascicular nucleus, magnocellular part

SPFm Ppp1r17-Cre_NL146

292480129 -2.06 0.25 4.15 0

Subparafascicular nucleus, parvicellular part

SPFp C57BL/6J 127396051 -2.92 1.75 3.45 0

Subparafascicular nucleus, parvicellular part

SPFp C57BL/6J 174583187 -3.28 2.00 3.20 0

Subparafascicular nucleus, parvicellular part

SPFp Calb2-IRES-Cre 287880821 -2.92 1.75 3.45 0

Subparafascicular nucleus, parvicellular part

SPFp Calb2-IRES-Cre 301063301 -2.92 1.75 3.45 0

Subparafascicular nucleus, parvicellular part

SPFp Th-Cre_FI172 266501422 -2.92 1.75 3.45 0

Subparaventricular zone SBPV Oxtr-Cre_ON66 299408890 -0.58 0.20 4.75 0

Substantia innominata SI C57BL/6J 125436508 1.10 1.50 5.15 0

Substantia innominata SI C57BL/6J 273026584 0.62 1.20 4.90 0

Substantia innominata SI Chat-IRES-Cre 126711445 -0.58 1.75 4.50 0

Substantia innominata SI Chat-IRES-Cre 126841788 0.02 1.60 4.55 0

Substantia innominata SI Chrna2-Cre_OE25

304762245 1.10 1.50 5.15 0

Substantia innominata SI Chrna2-Cre_OE25

304970618 -0.94 2.25 4.47 0

Substantia innominata SI Crh-IRES-Cre (BL)

278179088 -0.94 2.25 4.47 0

Substantia innominata SI Drd3-Cre_KI196 300111087 -1.82 2.65 4.25 0

Substantia innominata SI Drd3-Cre_KI196 305026861 0.62 1.20 4.85 0

Page 103: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 103 of 117

Substantia innominata SI Efr3a-Cre_NO108

298835152 0.14 2.07 4.76 0

Substantia innominata SI Ntrk1-IRES-Cre 299404532 -0.58 1.75 4.50 0

Substantia innominata SI Slc17a6-IRES-Cre

302739608 0.62 1.20 4.85 0

Substantia nigra, compact part SNc Calb2-IRES-Cre 301062306 -1.70 1.40 4.85 0

Substantia nigra, compact part SNc Gad2-IRES-Cre 303534443 -3.28 1.50 4.30 0

Substantia nigra, compact part SNc Slc18a2-Cre_OZ14

292958638 -3.08 1.25 4.15 0

Substantia nigra, compact part SNc Slc6a3-Cre 160539283 -3.08 1.25 4.08 0

Substantia nigra, reticular part SNr C57BL/6J 100141993 -3.28 1.50 4.30 0

Substantia nigra, reticular part SNr C57BL/6J 158914182 -3.08 1.25 4.30 0

Substantia nigra, reticular part SNr C57BL/6J 175263063 -3.40 1.60 4.60 0

Substantia nigra, reticular part SNr Pvalb-IRES-Cre 299895444 -3.28 1.50 4.30 0

Subthalamic nucleus STN A930038C07Rik-Tg1-Cre

264697714 -1.70 1.40 4.85 0

Subthalamic nucleus STN C57BL/6J 146986331 -1.34 1.75 4.50 0

Subthalamic nucleus STN C57BL/6J 174788109 -1.82 2.05 4.25 0

Superior central nucleus raphe CS C57BL/6J 156929391 -4.36 0.30 4.50 0

Superior central nucleus raphe CS Slc18a2-Cre_OZ14

300689439 -4.84 0.22 3.85 0

Superior colliculus, motor related SCm C57BL/6J 126523066 -4.48 0.50 1.85 0

Superior colliculus, motor related SCm C57BL/6J 126646502 -3.80 0.30 1.20 0

Superior colliculus, motor related SCm C57BL/6J 128001349 -4.36 1.25 1.20 0

Superior colliculus, motor related SCm C57BL/6J 146078721 -3.80 1.50 1.77 0

Superior colliculus, motor related SCm C57BL/6J 175158132 -3.80 1.50 2.10 0

Superior colliculus, motor related SCm Gad2-IRES-Cre 266646036 -2.92 1.25 2.76 0

Page 104: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 104 of 117

Superior colliculus, motor related SCm Nos1-CreERT2 305025440 -4.36 0.50 1.00 0

Superior colliculus, motor related SCm Pdzk1ip1-Cre_KD31

167118084 -2.92 1.25 2.76 0

Superior colliculus, motor related SCm Pdzk1ip1-Cre_KD31

182029881 -2.70 0.56 1.92 0

Superior colliculus, motor related SCm Pdzk1ip1-Cre_KD31

183376269 -2.70 0.56 1.92 0

Superior colliculus, motor related SCm Ppp1r17-Cre_NL146

278513131 -4.36 0.30 0.94 0

Superior colliculus, motor related SCm Ppp1r17-Cre_NL146

292533477 -0.82 1.13 3.28 0

Superior colliculus, motor related SCm Ppp1r17-Cre_NL146

307656580 -3.80 1.50 1.77 0

Superior colliculus, motor related SCm Ppp1r17-Cre_NL146

307691605 -4.36 0.30 0.94 0

Superior colliculus, motor related SCm Pvalb-IRES-Cre 182613651 -4.36 0.50 2.01 0

Superior colliculus, motor related SCm Slc17a6-IRES-Cre

294175704 -2.80 0.25 2.40 0

Superior colliculus, motor related SCm Slc17a6-IRES-Cre

305426208 -3.16 1.60 2.85 0

Superior colliculus, sensory related SCs C57BL/6J 112827164 -4.36 0.30 0.94 0

Superior colliculus, sensory related SCs C57BL/6J 114754390 -3.52 0.60 1.07 0

Superior colliculus, sensory related SCs Gad2-IRES-Cre 292211743 -4.72 1.25 1.10 0

Superior colliculus, sensory related SCs Pdzk1ip1-Cre_KD31

176900059 -3.52 0.60 1.25 0

Superior colliculus, sensory related SCs Ppp1r17-Cre_NL146

278511717 -4.36 1.25 1.20 0

Superior colliculus, sensory related SCs Ppp1r17-Cre_NL146

287459601 -3.80 0.30 1.20 0

Superior colliculus, sensory related SCs Rorb-IRES2-Cre 304338014 -3.52 0.60 1.25 0

Page 105: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 105 of 117

Superior olivary complex, lateral part SOCl Nxph4-2A-CreERT2

287668550 0.00 calamus

(-7.32 bregma)

0.05 0.20 0

Supplemental somatosensory area SSs A930038C07Rik-Tg1-Cre

286834976 -0.70 4.00, 3.50 1.70 0

Supplemental somatosensory area SSs C57BL/6J 100149969 1.10 3.25, 3.00 1.24, 1.69

0

Supplemental somatosensory area SSs C57BL/6J 112514915 -0.70 3.88, 3.38 1.66 0

Supplemental somatosensory area SSs C57BL/6J 113036264 -0.22 3.88, 3.38 1.65 0

Supplemental somatosensory area SSs C57BL/6J 117298988 -0.82 3.90 1.75 0

Supplemental somatosensory area SSs C57BL/6J 174360333 0.26 3.65 1.85 0

Supplemental somatosensory area SSs C57BL/6J 180717881 0.74 3.30 1.63 0

Supplemental somatosensory area SSs Chrna2-Cre_OE25

297945448 -0.70 4.00, 3.50 1.70 0

Supplemental somatosensory area SSs Cux2-IRES-Cre 278315824 -0.70 4.00, 3.50 1.70 0

Supplemental somatosensory area SSs Cux2-IRES-Cre 287951098 -0.22 3.88, 3.38 1.66 0

Supplemental somatosensory area SSs Cux2-IRES-Cre 297855879 -0.70 4.00, 3.50 1.70 0

Supplemental somatosensory area SSs Efr3a-Cre_NO108

287996596 -0.70 4.00, 3.50 1.70 0

Supplemental somatosensory area SSs Efr3a-Cre_NO108

301178953 -0.22 3.38, 3.88 1.66 0

Supplemental somatosensory area SSs Nr5a1-Cre 266175461 -0.22 3.88, 3.38 1.66 0

Supplemental somatosensory area SSs Ntsr1-Cre_GN220

159552290 -0.70 3.88, 3.38 1.66 0

Supplemental somatosensory area SSs Ntsr1-Cre_GN220

159750477 1.10 3.25, 3.00 1.90, 2.35

0

Supplemental somatosensory area SSs Oxtr-Cre_ON66 286838022 -0.22 3.40 3.25 0

Supplemental somatosensory area SSs Rbp4-Cre_KL100 168163498 -0.70 3.88, 3.38 1.66 0

Page 106: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 106 of 117

Supplemental somatosensory area SSs Rbp4-Cre_KL100 286314623 -0.22 3.88, 3.38 1.66 0

Supplemental somatosensory area SSs Rorb-IRES2-Cre 301580339 -0.70 3.5, 4.0 1.70 0

Supplemental somatosensory area SSs Scnn1a-Tg3-Cre 257636467 -0.70 4.00, 3.50 1.70 0

Supplemental somatosensory area SSs Slc18a2-Cre_OZ14

268042502 -0.70 4.00, 3.50 1.70 0

Supplemental somatosensory area SSs Slc18a2-Cre_OZ14

287039061 -0.70 4.00, 3.50 1.70 0

Supplemental somatosensory area SSs Syt6-Cre_KI148 159508775 -0.70 3.88, 3.38 1.66 0

Supplemental somatosensory area SSs Syt6-Cre_KI148 299829181 -0.22 3.38, 3.88 1.66 0

Supplemental somatosensory area SSs Tlx3-Cre_PL56 303616833 -0.22 3.38, 3.88 1.66 0

Suprachiasmatic nucleus SCH Avp-IRES2-Cre 287665706 -0.34 0.20 5.60 0

Suprachiasmatic nucleus SCH Ppp1r17-Cre_NL146

286727483 -0.34 0.20 5.60 0

Suprachiasmatic nucleus SCH Rorb-IRES2-Cre 304473503 -4.36 0.50 1.00 0

Suprachiasmatic nucleus SCH Vip-IRES-Cre 293431163 -0.34 0.20 5.60 0

Suprageniculate nucleus SGN Slc18a2-Cre_OZ14

300688721 -3.16 2.10 2.85 0

Supramammillary nucleus SUM C57BL/6J 273055501 -2.35 0.13 5.30 0

Supramammillary nucleus SUMm Nos1-CreERT2 304947804 -2.80 0.25 4.90 0

Supramammillary nucleus, lateral part SUMl C57BL/6J 158314987 -2.80 0.25 4.90 0

Supramammillary nucleus, lateral part SUMl Hdc-Cre_IM1 157952778 -2.46 1.00 5.30 0

Supramammillary nucleus, lateral part SUMl Hdc-Cre_IM1 175736945 -2.46 1.00 5.30 0

Supramammillary nucleus, lateral part SUMl Nxph4-2A-CreERT2

304720741 -2.70 0.13 5.20 0

Supraoptic nucleus SO Avp-IRES2-Cre 286726065 -0.46 1.15 5.45 0

Supraoptic nucleus SO Avp-IRES2-Cre 287666431 -0.46 1.15 5.45 0

Supraoptic nucleus SO Oxt-IRES-Cre 147790922 -0.58 1.13 5.40 0

Page 107: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 107 of 117

Supraoptic nucleus SO Oxt-IRES-Cre 147968866 -0.58 1.13 5.40 0

Supraoptic nucleus SO Oxt-IRES-Cre 178488152 -0.58 1.13 5.40 0

Taenia tecta, dorsal part TTd C57BL/6J 133286030 2.34 0.40 2.89 0

Taenia tecta, dorsal part TTd C57BL/6J 141601779 1.70 0.40 2.00 0

Taenia tecta, dorsal part TTd Cnnm2-Cre_KD18

167029528 1.34 0.10 2.80 0

Taenia tecta, dorsal part TTd Kcnc2-Cre 176899332 2.34 0.40 2.89 0

Tegmental reticular nucleus TRN C57BL/6J 121145045 -4.16 0.25 4.90 0

Tegmental reticular nucleus TRN C57BL/6J 147135812 -4.16 0.25 5.15 0

Tegmental reticular nucleus TRN Crh-IRES-Cre (BL)

293752263 -4.72 0.25 4.40 0

Tegmental reticular nucleus TRN Gabrr3-Cre_KC112

263976175 -4.16 0.25 5.60 0

Tegmental reticular nucleus TRN Gabrr3-Cre_KC112

301875966 -4.04 0.25 5.90 0

Temporal association areas TEa A930038C07Rik-Tg1-Cre

176429574 -4.36 4.00 1.25 0

Temporal association areas TEa A930038C07Rik-Tg1-Cre

298350922 -4.36 4.25 1.35 0

Temporal association areas TEa C57BL/6J 114250546 -4.60 3.60 0.55 0

Temporal association areas TEa C57BL/6J 127089669 -4.16 3.85 0.90 0

Temporal association areas TEa C57BL/6J 157062358 0.62 2.90 3.75 0

Temporal association areas TEa Chrna2-Cre_OE25

292208876 -4.36 4.25 1.35 0

Temporal association areas TEa Cux2-IRES-Cre 287953929 -4.60 3.80 0.45 30

Temporal association areas TEa Cux2-IRES-Cre 293470216 -4.36 4.00 1.25 0

Temporal association areas TEa Ntsr1-Cre_GN220

159321806 -4.36 4.00 1.25 0

Page 108: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 108 of 117

Temporal association areas TEa Ntsr1-Cre_GN220

170261951 -4.04 4.00 0.35, 0.75

30

Temporal association areas TEa Ntsr1-Cre_GN220

298830868 -4.26 3.40 2.2, 2.6

0

Temporal association areas TEa Rbp4-Cre_KL100 166083557 -4.16 3.75 0.81 0

Temporal association areas TEa Rbp4-Cre_KL100 167027666 -4.36 4.00 1.25 0

Temporal association areas TEa Rbp4-Cre_KL100 298178204 -4.16 3.95 0.85 0

Temporal association areas TEa Syt6-Cre_KI148 156786939 -4.16 3.75 0.81 0

Temporal association areas TEa Syt6-Cre_KI148 158141324 -4.36 4.00 1.25 0

Temporal association areas TEa Tlx3-Cre_PL56 294516943 -4.36 4.00 1.25 0

Triangular nucleus of septum TRS C57BL/6J 125830911 -0.10 0.10 2.30 0

Tuberal nucleus TU Avp-IRES2-Cre 267396430 -0.58 1.15 5.50 0

Tuberal nucleus TU Avp-IRES2-Cre 267397226 -0.58 1.15 5.50 0

Tuberal nucleus TU Esr1-2A-Cre 176886958 -1.50 0.78 5.75 0

Tuberal nucleus TU Esr1-2A-Cre 264320076 -1.50 0.78 5.76 0

Tuberomammillary nucleus, ventral part TMv Hdc-Cre_IM1 157952068 -2.46 0.55 5.65 0

Ventral anterior-lateral complex of the thalamus

VAL C57BL/6J 100142569 -0.82 1.13 3.28 0

Ventral anterior-lateral complex of the thalamus

VAL C57BL/6J 113884251 -0.70 1.53 3.48 0

Ventral anterior-lateral complex of the thalamus

VAL Gal-Cre_KI87 156393801 -0.58 3.40 4.94 40

Ventral anterior-lateral complex of the thalamus

VAL Grik4-Cre 300237470 -0.70 1.53 3.48 0

Ventral anterior-lateral complex of the thalamus

VAL Prkcd-GluCla-CFP-IRES-Cre

292321278 -0.82 1.13 3.28 0

Ventral anterior-lateral complex of the thalamus

VAL Slc17a6-IRES-Cre

310193233 -1.34 0.85 3.97 0

Page 109: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 109 of 117

Ventral auditory area AUDv C57BL/6J 112881858 -2.80 4.40 1.60 0

Ventral auditory area AUDv Tlx3-Cre_PL56 303582161 -2.46 4.35 0.85 0

Ventral cochlear nucleus VCO C57BL/6J 272825299 -5.52 2.50 3.65 0

Ventral cochlear nucleus VCO Ntrk1-IRES-Cre 265135682 -5.52 2.50 3.65 0

Ventral cochlear nucleus VCO Pvalb-IRES-Cre 167211503 -5.52 2.50 3.65 0

Ventral medial nucleus of the thalamus VM C57BL/6J 174736554 -1.46 0.80 4.25 0

Ventral medial nucleus of the thalamus VM C57BL/6J 180707817 -1.46 0.80 4.25 0

Ventral medial nucleus of the thalamus VM Cck-IRES-Cre 277849256 -3.80 0.04 2.85 0

Ventral medial nucleus of the thalamus VM Cck-IRES-Cre 306444486 -1.50 0.35 5.30 0

Ventral medial nucleus of the thalamus VM Gabrr3-Cre_KC112

170859382 -1.34 0.95 4.55 0

Ventral medial nucleus of the thalamus VM Ppp1r17-Cre_NL146

268205344 -1.34 0.85 3.97 0

Ventral medial nucleus of the thalamus VM Prkcd-GluCla-CFP-IRES-Cre

267929554 -1.34 0.85 3.97 0

Ventral medial nucleus of the thalamus VM Prkcd-GluCla-CFP-IRES-Cre

278067445 -1.34 0.32 4.05 0

Ventral part of the lateral geniculate complex

LGv C57BL/6J 147212977 -2.30 2.55 3.00 0

Ventral part of the lateral geniculate complex

LGv Pdzk1ip1-Cre_KD31

157765542 -2.30 2.55 3.00 0

Ventral part of the lateral geniculate complex

LGv Ppp1r17-Cre_NL146

278398949 -2.80 2.85 3.00 0

Ventral part of the lateral geniculate complex

LGv Slc32a1-IRES-Cre

267538006 -2.46 2.60 2.36 0

Ventral part of the lateral geniculate complex

LGv Sst-IRES-Cre 299623794 -2.30 2.55 3.00 0

Ventral posterolateral nucleus of the thalamus

VPL C57BL/6J 158375425 -1.70 1.90 3.40 0

Page 110: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 110 of 117

Ventral posterolateral nucleus of the thalamus

VPL Grik4-Cre 287446625 -0.70 1.53 3.48 0

Ventral posterolateral nucleus of the thalamus

VPL Grik4-Cre 287447332 -1.22 2.00 3.09 0

Ventral posterolateral nucleus of the thalamus

VPL Grik4-Cre 301877386 -1.22 2.00 3.09 0

Ventral posterolateral nucleus of the thalamus

VPL Scnn1a-Tg2-Cre 156202272 -1.70 1.90 3.40 0

Ventral posteromedial nucleus of the thalamus

VPM C57BL/6J 100141223 -1.34 0.85 3.97 0

Ventral posteromedial nucleus of the thalamus

VPM C57BL/6J 180601025 -1.46 2.20 3.09 0

Ventral posteromedial nucleus of the thalamus

VPM Gal-Cre_KI87 182515576 -1.82 1.50 3.25 0

Ventral posteromedial nucleus of the thalamus

VPM Gal-Cre_KI87 278070717 -2.00 2.15 2.60 0

Ventral posteromedial nucleus of the thalamus

VPM Ppp1r17-Cre_NL146

268206050 -1.70 1.90 3.40 0

Ventral posteromedial nucleus of the thalamus

VPM Ppp1r17-Cre_NL146

268399868 -1.82 1.60 3.30 0

Ventral posteromedial nucleus of the thalamus

VPM Scnn1a-Tg2-Cre 156202979 -1.82 1.50 3.25 0

Ventral posteromedial nucleus of the thalamus

VPM Slc17a6-IRES-Cre

312240825 -1.70 1.90 3.40 0

Ventral posteromedial nucleus of the thalamus, parvicellular part

VPMpc Ppp1r17-Cre_NL146

278509488 -1.94 0.90 5.00 0

Ventral posteromedial nucleus of the thalamus, parvicellular part

VPMpc Scnn1a-Tg2-Cre 162018169 -2.06 0.45 4.00 0

Ventral posteromedial nucleus of the thalamus, parvicellular part

VPMpc Scnn1a-Tg2-Cre 162018879 -1.94 1.10 4.00 0

Ventral premammillary nucleus PMv Avp-IRES2-Cre 267398651 -1.58 0.75 5.75 0

Page 111: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 111 of 117

Ventral premammillary nucleus PMv Lepr-IRES-Cre 167656152 -2.46 0.55 5.65 0

Ventral premammillary nucleus PMv Slc6a3-Cre 263780018 -2.46 0.55 5.65 0

Ventral premammillary nucleus PMv Tac1-IRES2-Cre 299654968 -1.46 0.39 5.50 0

Ventral premammillary nucleus PMv Th-Cre_FI172 286728896 -1.70 0.20 5.90 0

Ventral tegmental area VTA C57BL/6J 126710740 -2.46 0.55 5.65 0

Ventral tegmental area VTA C57BL/6J 127796728 -2.55 0.13 4.55 0

Ventral tegmental area VTA Cck-IRES-Cre 171021829 -3.28 0.36 4.13 0

Ventral tegmental area VTA Chrna2-Cre_OE25

278178382 -3.52 0.28 4.30 0

Ventral tegmental area VTA Erbb4-2A-CreERT2

127867804 -3.28 0.36 4.13 0

Ventral tegmental area VTA Erbb4-2A-CreERT2

165975096 -3.28 0.36 4.13 0

Ventral tegmental area VTA Gabrr3-Cre_KC112

300166697 -2.80 0.25 4.90 0

Ventral tegmental area VTA Nos1-CreERT2 304720034 -2.46 0.55 5.65 0

Ventral tegmental area VTA Pdzk1ip1-Cre_KD31

166054222 -3.28 0.36 4.13 0

Ventral tegmental area VTA Slc17a6-IRES-Cre

302087552 -2.30 0.25 4.37 0

Ventral tegmental area VTA Slc18a2-Cre_OZ14

287492899 -2.80 0.80 5.15 0

Ventral tegmental area VTA Slc18a2-Cre_OZ14

301732962 -3.28 0.36 4.13 0

Ventral tegmental area VTA Slc6a3-Cre 160540751 -3.28 0.36 4.13 0

Ventral tegmental area VTA Syt17-Cre_NO14 127798146 -3.28 0.36 4.13 0

Ventral tegmental area VTA Th-Cre_FI172 304337288 -3.28 0.36 4.13 0

Ventral tegmental area VTA Th-IRES-CreER 156314762 -3.28 0.36 4.13 0

Page 112: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 112 of 117

Ventromedial hypothalamic nucleus VMH Adcyap1-2A-Cre 303708513 -1.46 0.39 5.50 0

Ventromedial hypothalamic nucleus VMH C57BL/6J 157549402 -0.70 0.37 5.40 0

Ventromedial hypothalamic nucleus VMH C57BL/6J 175106769 -0.70 0.40 5.46 0

Ventromedial hypothalamic nucleus VMH C57BL/6J 277615922 -0.70 0.40 5.55 0

Ventromedial hypothalamic nucleus VMH Erbb4-2A-CreERT2

277854916 -1.70 0.20 5.90 0

Ventromedial hypothalamic nucleus VMH Esr1-2A-Cre 176888661 -1.50 0.78 5.75 0

Ventromedial hypothalamic nucleus VMH Esr1-2A-Cre 264248605 -1.50 0.78 5.76 0

Ventromedial hypothalamic nucleus VMH Esr1-2A-Cre 264319363 -1.50 0.78 5.76 0

Ventromedial hypothalamic nucleus VMH Fezf1-2A-dCre 267540168 -1.46 0.39 5.50 0

Ventromedial hypothalamic nucleus VMH Fezf1-2A-dCre 292211026 -1.46 0.39 5.50 0

Ventromedial hypothalamic nucleus VMH Ins2-Cre 286319033 -1.46 0.39 5.50 0

Ventromedial hypothalamic nucleus VMH Nr5a1-Cre 114290225 -1.46 0.39 5.30 0

Ventromedial hypothalamic nucleus VMH Nr5a1-Cre 182337561 -1.46 0.39 5.30 0

Ventromedial hypothalamic nucleus VMH Slc17a6-IRES-Cre

286556208 -1.50 0.35 5.30 0

Ventromedial hypothalamic nucleus VMH Sst-IRES-Cre 304948510 -1.58 0.75 5.75 0

Visceral area VISC C57BL/6J 180074890 -1.22 4.00 2.60 0

Visceral area VISC C57BL/6J 180917660 -0.58 4.20 2.15 0

Visceral area VISC Rbp4-Cre_KL100 249402048 1.10 3.25, 3.00 1.90, 2.35

0

Visceral area VISC Syt6-Cre_KI148 177783918 1.10 3.25, 3.00 1.90, 2.35

0

Zona incerta ZI C57BL/6J 113095845 -2.18 1.75 4.12 0

Zona incerta ZI C57BL/6J 126190743 -1.70 1.40 4.45 0

Zona incerta ZI C57BL/6J 127797441 -1.34 0.95 4.55 0

Page 113: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 113 of 117

Zona incerta ZI C57BL/6J 157063074 -3.52 2.50 1.35 0

Zona incerta ZI C57BL/6J 175018829 -2.70 1.50 3.50 0

Zona incerta ZI Cart-Tg1-Cre 266174751 -1.50 0.35 5.20 0

Zona incerta ZI Drd3-Cre_KI196 304858700 -2.18 1.75 4.12 0

Zona incerta ZI Gabrr3-Cre_KC112

170263370 -1.70 1.40 4.45 0

Zona incerta ZI Gabrr3-Cre_KC112

170858675 -2.18 1.75 4.12 0

Zona incerta ZI Gad2-IRES-Cre 156315468 -1.34 0.95 4.55 0

Zona incerta ZI Gad2-IRES-Cre 286662551 -2.18 1.75 4.12 0

Zona incerta ZI Gad2-IRES-Cre 305321883 -1.70 1.40 4.85 0

Zona incerta A13 Lypd6-Cre_KL156

299760587 -1.34 1.00 4.84 0

Zona incerta ZI Pvalb-IRES-Cre 301539438 -2.18 1.75 4.12 0

Zona incerta ZI Slc17a6-IRES-Cre

168663472 -1.70 1.40 4.45 0

Zona incerta ZI Slc32a1-IRES-Cre

171065906 -2.18 1.75 4.12 0

Zona incerta ZI Slc32a1-IRES-Cre

171066613 -1.34 0.95 4.55 0

Zona incerta ZI Slc32a1-IRES-Cre

305379705 -1.70 1.40 4.85 0

Zona incerta ZI Tac1-IRES2-Cre 300923916 -0.80 0.25 4.85 0

Zona incerta ZI Th-Cre_FI172 306270474 -1.34 0.95 4.55 0

* For the majority of target sites, the anterior/posterior (AP) coordinates are referenced from Bregma, the medial/lateral (ML) coordinates are distance

from midline at Bregma, and dorsal/ventral (DV) coordinates are measured from the pial surface of the brain. For several of the caudal-most medullary

nuclei (e.g. gracile nucleus and spinal nucleus of the trigeminal, caudal part), the calamus (at the floor of the 4th ventricle) is used as a registration

point instead of Bregma.

Page 114: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 114 of 117

Table 2. Stereotaxic coordinates used for BDA vs. rAAV comparison.

Brain region (primary structure infected by rAAV)

Reference atlas acronym

Mouse strain Experiment ID AP ML DV Angle°

Anterior olfactory nucleus AON C57BL/6J 100142693 2.96 1.14 2.67 0

Anterior olfactory nucleus AON C57BL/6J 100144288 2.96 1.14 2.67 0

Anterior olfactory nucleus AON C57BL/6J 100147358 2.96 1.14 2.67 0

Caudoputamen CP C57BL/6J 100142699 -0.34 1.90 3.40 0

Caudoputamen CP C57BL/6J 100142293 0.74 1.75 2.60 0

Caudoputamen CP C57BL/6J 100144295 0.74 1.75 2.60 0

Caudoputamen CP C57BL/6J 100145836 0.74 1.75 2.60 0

Caudoputamen CP B6129SF1/J 112311239 -0.34 1.90 3.40 0

Caudoputamen CP B6129SF1/J 159609527 0.74 1.75 2.60 0

Caudoputamen CP B6129SF1/J 183568601 0.74 1.75 2.60 0

Field CA1 CA1 C57BL/6J 100141775 -1.94 1.00 1.30 0

Field CA1 CA1 C57BL/6J 100141772 -1.94 1.00 1.30 0

Field CA1 CA1 B6129SF1/J 113067695 -1.94 1.00 1.30 0

Gigantocellular reticular nucleus

GRN C57BL/6J 100142687 -7.20 0.50 4.75 0

Globus pallidus, external segment

GPe C57BL/6J 100141804 -0.34 1.90 3.40 0

Inferior colliculus, external nucleus

ICe C57BL/6J 100145841 -4.36 1.59 1.87 0

Intermediate reticular nucleus IRN C57BL/6J 100144286 -7.20 0.50 4.75 0

Kolliker-Fuse subnucleus KF C57BL/6J 100142301 -5.20 1.40 3.58 0

Lateral hypothalamic area LHA C57BL/6J 100141800 -1.06 1.00 4.75 0

Page 115: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 115 of 117

Brain region (primary structure infected by rAAV)

Reference atlas acronym

Mouse strain Experiment ID AP ML DV Angle°

Lateral hypothalamic area LHA C57BL/6J 100147352 -1.06 1.12 4.88 0

Lateral hypothalamic area LHA C57BL/6J 100142700 -1.06 1.00 4.75 0

Lateral hypothalamic area LHA B6129SF1/J 113066020 -1.06 1.00 4.75 0

Lateral hypothalamic area LHA C57BL/6J 159616564 -0.70 1.12 5.00 0

Lateral posterior nucleus of the thalamus

LP C57BL/6J 112296535 -2.30 2.00 2.45 0

Lateral posterior nucleus of the thalamus

LP C57BL/6J 100141798 -2.30 2.00 2.45 0

Lateral septal nucleus LS B6129SF1/J 100147797 0.14 0.50 2.80 0

Lateral septal nucleus LS C57BL/6J 159617389 0.14 0.50 2.80 0

Lateral septal nucleus, caudal (caudodorsal) part

LSc C57BL/6J 112312484 0.14 0.50 2.80 0

Lateral septal nucleus, rostral (rostroventral) part

LSr C57BL/6J 100142294 0.14 0.50 2.80 0

Lobules IV-V CUL 4,5 C57BL/6J 100145843 -5.88 0.50 0.40 0

Lobules IV-V CUL4, 5 C57BL/6J 100147373 -6.24 0.50 0.94 0

Lobules IV-V CUL4, 5 C57BL/6J 100147369 -6.24 0.50 0.94 0

Lobules IV-V CUL4, 5 C57BL/6J 100147375 -6.24 0.50 0.94 0

Medullary reticular nucleus, ventral part

MDRNv C57BL/6J 100145829 -7.20 0.50 4.75 0

Midbrain reticular nucleus MRN C57BL/6J 100142300 -3.40 0.75 3.60 0

Midbrain reticular nucleus MRN C57BL/6J 100143833 -3.40 0.75 3.60 0

Midbrain reticular nucleus MRN C57BL/6J 100145833 -3.40 0.75 3.60 0

Page 116: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 116 of 117

Brain region (primary structure infected by rAAV)

Reference atlas acronym

Mouse strain Experiment ID AP ML DV Angle°

Midbrain reticular nucleus MRN C57BL/6J 100142704 -3.28 1.50 4.30 0

Posterior complex of the thalamus

PO C57BL/6J 112297892 -1.82 1.50 3.25 0

Posterior complex of the thalamus

PO B6129SF1/J 113066858 -1.82 1.50 3.25 0

Primary motor area MOp C57BL/6J 100141268 1.54 1.60 0.40, 0.80 0

Primary motor area MOp C57BL/6J 100145496 1.54 1.60 0.40, 0.80 0

Primary motor area MOp C57BL/6J 100142689 1.54 1.60 0.40, 0.80 0

Primary motor area MOp B6129SF1/J 100147371 1.54 1.60 0.40, 0.80 0

Primary motor area MOp C57BL/6J 159613261 1.54 1.60 0.40, 0.80 0

Primary somatosensory area, barrel field

SSp-bfd C57BL/6J 100141261 -1.46 3.25 0.40, 0.80 20

Primary somatosensory area, barrel field

SSp-bfd C57BL/6J 100142701 -1.46 3.25 0.35, 0.80 20

Primary somatosensory area, barrel field

SSp-bfd C57BL/6J 159611609 -1.46 3.25 0.40, 0.80 20

Primary somatosensory area, trunk

SSp-tr C57BL/6J 100147356 -1.46 3.25 0.40, 0.80 20

Primary somatosensory area, trunk

SSp-tr B6129SF1/J 159610371 -1.46 3.25 0.40, 0.80 20

Primary visual area VISp C57BL/6J 100141263 -4.16 2.75 0.45 10

Primary visual area VISp C57BL/6J 100141777 -4.16 2.75 0.45 10

Primary visual area VISp C57BL/6J 100144292 -4.16 2.75 0.45 10

Primary visual area VISp C57BL/6J 159609113 -4.16 2.75 0.45 10

Primary visual area VISp C57BL/6J 159614086 -4.16 2.75 0.45 10

Page 117: Allen Mouse Brain Connectivity Atlas - Allen Brain Atlashelp.brain-map.org/download/attachments/2818171/... · 2017-10-03 · TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity

TECHNICAL WHITE PAPER Allen Mouse Brain Connectivity Atlas

MARCH 2016 v.9 alleninstitute.org

Injection Sites and Stereotaxic Coordinates brain-map.org

page 117 of 117

Brain region (primary structure infected by rAAV)

Reference atlas acronym

Mouse strain Experiment ID AP ML DV Angle°

Primary visual area VISp B6129SF1/J 159612434 -4.16 2.75 0.45 10

Septofimbrial nucleus SF C57BL/6J 100141266 0.14 0.50 2.80 0

Septofimbrial nucleus SF B6129SF1/J 112296088 -1.46 3.25 0.40, 0.80 20

Subiculum SUB C57BL/6J 100142710 -2.92 1.17 1.40 0

Subiculum SUB C57BL/6J 100145827 -2.92 1.17 1.40 0

Subiculum SUB C57BL/6J 112314965 -2.92 1.17 1.40 0

Substantia innominata SI B6129SF1/J 113071071 -1.22 2.75 3.80 0

Substantia nigra, compact part SNc C57BL/6J 100147802 -3.28 1.50 4.30 0

Substantia nigra, reticular part SNr C57BL/6J 100142698 -3.28 1.50 4.30 0

Substantia nigra, reticular part SNr C57BL/6J 112302860 -3.28 1.50 4.30 0

Superior colliculus, motor related

SCm C57BL/6J 100143837 -4.36 1.59 1.87 0

Superior colliculus, motor related

SCm C57BL/6J 100142302 -4.36 1.59 1.87 0

Superior colliculus, motor related

SCm B6129SF1/J 113072328 -4.36 1.59 1.87 0

Superior colliculus, sensory related

SCs C57BL/6J 100142706 -4.36 0.50 0.42 0

Ventral posteromedial nucleus of the thalamus

VPM C57BL/6J 100143831 -1.82 1.50 3.25 0

Ventral posteromedial nucleus of the thalamus

VPM C57BL/6J 100149111 -1.82 1.50 3.25 0

* For most cases presented, the anatomical area(s) of tracer uptake are well matched. However, there are cases with considerable differences in the

uptake area between BDA and rAAV due to uneven infection or leakage along the needle tract into neighboring anatomical regions. In such cases, the

primary structure infected by rAAV or BDA is listed separately on the website.