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SUPPLEMENTARY INFORMATIONdoi:10.1038/nature25193

Supplementary Figure 1– Flow cytometric gating strategies for hematopoietic cell populations Table of Content: Figure 1: Lin-, LSK, LS-K, HSC, MPP1-4 Figure 2: CLP, CMP, GMP, MEP Figure 3: Gran, B, B220high, B220int, T, CD4+ T-Cells, CD8+ T cells, RBC, EryA, EryB, EryC, Mgk Figure 4: PreProB, ProB PreB, trans B, mature B Figure 5: DN1, DN2, DN3, DN4, DN, DP, SP CD4, SP CD8 Figure 6: MLL-AF9 blasts Figure 7: in vivo reconstitution – peripheral blood Figure 8: in vivo reconstitution – bone marrow: HSC, MPP1-4 Figure 9: in vivo reconstitution – bone marrow: CLP, CMP, GMP, MEP Figure 10: in vivo reconstitution – bone marrow: Gran, B, EryA Figure 11: in vivo reconstitution – bone marrow: CD4+ T cells, CD8+ T cells, Mgk

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RESEARCHSupplementary Information File – Gating Strategies Figure 1: Gating strategies for Lin-, LSK, LS-K, HSC, MPP1-4

to define CD34+ and CD135+ Same Gates used for HSC and MPP gates

Notes: In some of the experiments the fluorophores used for c-Kit and Sca-1 were switched: c-Kit in APC and Sca-1 in APC-Cy7. All cell populations were backgated to ensure correct identification of target populations.

from bone marrow

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SUPPLEMENTARY INFORMATION RESEARCHSupplementary Information File – Gating Strategies Figure 2: CLP, CMP, GMP, MEP

Notes: In some of the experiments the fluorophores used for c-Kit and Sca-1 were switched: c-Kit in APC and Sca-1 in APC-Cy7. All cell populations were backgated to ensure correct identification of target populations.

from bone marrow

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RESEARCHSupplementary Information File – Gating Strategies Figure 3: Gran, B, B220high, B220int, T, CD4+ T-Cells, CD8+ T cells, RBC, EryA, EryB, EryC, Mgk

Notes: For total B cells the gates “B220high” and “B220int” were combined All cell populations were backgated to ensure correct identification of target populations.

from bone marrow

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SUPPLEMENTARY INFORMATION RESEARCHSupplementary Information File – Gating Strategies Figure 4: PreProB, ProB PreB, trans B, mature B

Notes: For mature B cells the gates “Early mature B” and “Late mature B” were combined All cell populations were backgated to ensure correct identification of target populations.

from bone marrow

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RESEARCHSupplementary Information File – Gating Strategies Figure 5: DN1, DN2, DN3, DN4, DN, DP, SP CD4, SP CD8

Notes: All cell populations were backgated to ensure correct identification of target populations.

from thymus

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SUPPLEMENTARY INFORMATION RESEARCHSupplementary Information File – Gating Strategies Figure 6: MLL-AF9 blasts

Notes: All cell populations were backgated to ensure correct identification of target populations.

from peripheral blood (erythrocyte lysed)

GFP signal based on negativity in the CD45.1 cells (recipient bone marrow)

MLL-AF9-GFP+ CD45.2+ cells

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RESEARCHSupplementary Information File – Gating Strategies Figure 7: In vivo reconstitution - peripheral blood

Notes: All cell populations were backgated to ensure correct identification of target populations.

from peripheral blood (erythrocyte lysed)

CD45.1+ (recipient cells) CD45.2+ (donor cells) CD45.1+/CD45.2+ (competitor cells)

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SUPPLEMENTARY INFORMATION RESEARCHSupplementary Information File – Gating Strategies Figure 8: In vivo reconstitution – bone marrow: HSC, MPP1-4

Notes: All cell populations were backgated to ensure correct identification of target populations.

CD45.1+ (recipient cells) CD45.2+ (donor cells) CD45.1+/CD45.2+ (competitor cells)

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RESEARCHSupplementary Information File – Gating Strategies Figure 9: In vivo reconstitution – bone marrow: CLP, CMP, GMP, MEP

Notes: All cell populations were backgated to ensure correct identification of target populations.

from bone marrow

CD45.1+ (recipient cells) CD45.2+ (donor cells) CD45.1+/CD45.2+ (competitor cells)

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SUPPLEMENTARY INFORMATION RESEARCHSupplementary Information File – Gating Strategies Figure 10: In vivo reconstitution – bone marrow: EryA, Gran, B

Notes: All cell populations were backgated to ensure correct identification of target populations.

from bone marrow

CD45.1+ (recipient cells) CD45.2+ (donor cells) CD45.1+/CD45.2+ (competitor cells)

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RESEARCH

Supplementary Information File – Gating Strategies Figure 11: In vivo reconstitution – bone marrow: CD4+ T cells CD8+ T cells, Mgk

Notes: All cell populations were backgated to ensure correct identification of target populations.

from bone marrow

CD45.1+ (recipient cells) CD45.2+ (donor cells) CD45.1+/CD45.2+ (competitor cells)