Small samples. Big insights.

GeneChip® WT Pico Kit performance data

www.affymetrix.com/pico

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Introducing the newGeneChip® WT Pico Kit (WT Pico Kit)

WT Pico Kit is the most flexible and sensitive target preparation method for accurate and precise analysis of the transcriptome from limited and challenging samples on whole-transcriptome arrays from Affymetrix.

Reveal the biology in small subpopulations of cells.

Benefit from total flexibility with a single kit for

key sample types, including cultured cells, fresh/fresh frozen or formalin-fixed paraffin-embedded (FFPE) tissues, and whole blood, without

the need for globin or ribosomal RNA removal.

Obtain the highest accuracy with an assay that ensures strand specificity is preserved.

Perform multiple layers of analysis by combining with Clariom™ D arrays for transcriptome profiling

to accurately measure gene- and transcript-level expression of coding and long non-coding (lnc)RNA.

Kitted reagents for cells,

fresh/fresh frozen or

FFPE* tissue, and whole

blood, with as little as

100 pg of total RNA

(~10 cells).

*Minimum RNA input from FFPE samples is 500 pg.

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Incorporate WT Pico Kit into your expression workflow for limited and challenging samples

Clariom D arrays for human, mouse,

and rat

Transciptome Analysis Console (TAC)

Software

Isolate Prepare Measure Interpret

Isolate cell subpopulations with common techniques such as flow cytometry.

Prepare your sample from as little as 100 pg total RNA (~10 cells).

Obtain a detailed view of the transcriptome by measuring coding and non-coding genes, exons, and splice variants.

Analyze and visualize complexgene pathways, miRNA and target gene interactions, and alternative splicing events in minutes.

WT Pico Kit

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Using 500 pg and 100 pg RNA, WT Pico Kit produces results similar to 50 ng RNA

r=0.949r=0.952 r=0.892

MAQC A signal MAQC B signal MAQC A/B fold change

50

0 p

g

r=0.931r=0.942 r=0.827

10

0 p

gWT

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50 ng RNAWT PLUS Kit

MicroArray Quality Control Sample A (MAQC A) from Agilent Technologies and MAQC B from Ambion™, Thermo Fisher Scientific were prepared using WT Pico Kit and GeneChip® WT PLUS Reagent Kit (WT PLUS Kit)and analyzed on transcriptome profiling arrays from Affymetrix.

The ratio of gene-level expression of MAQC A/B at 500 pg and 100 pg total input RNA using WT Pico Kit was compared with 50 ng prepared usingWT PLUS Kit.

At 500 pg input RNA, WT Pico Kit has higher signal and fold change correlation with 50 ng RNA than target preparation methods from other suppliers, showing superior performance of WT Pico Kit.

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WT Pico Kit provides sufficient yields of cRNA and cDNA from FFPE samples

500 pg

WT Pico Kit

2 ng

500 pg

WT Pico Kit

2 ng

µg c

RN

Aµg c

DN

A

0

25

100

150

50

200

0

6

10

20

30

FFPE sample

RNA extraction(500 pg–2 ng input RNA)

cRNA(minimum yield

required >25 µg)

cDNA(minimum yield required >6 µg)

Fragment and label

Hybridization onto array

A target preparation kit needs to generate a minimum yield of 25 µg cRNA and 6 µg cDNA from extracted total RNA before hybridization onto Clariom™ whole-transcriptome arrays. WT Pico Kit exceeds the minimum yield specifications from a variety of RNA input amounts extracted from a range of FFPE tissues.

Sim

plifi

ed

WT

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ork

flo

w

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WT Pico Kit does not require a globin mRNA reduction step for whole-blood samples

Sam

ple

1

50 ngWT PLUS Kit

r=0.952 r=0.952

r=0.949 r=0.952

Sam

ple

2WT P

ico

Kit

50

0 p

g

Whole-blood samples

Globin mRNA-reduced blood samples

500 pg of total RNA from whole-blood samples prepared using WT Pico Kit generates a signal correlation with 50 ng total RNA that is nearly identical to globin mRNA-reduced blood samples at the same input amounts.

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WT Pico Kit outperforms other suppliers when working with limited input RNA

MAQC A signal MAQC B signal MAQC A/B fold change

WT

Pic

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it5

00

pg

Co

mp

an

y N

50

0 p

g

50 ng RNA WT PLUS Kit

r=0.952 r=0.949 r=0.892

r=0.935 r=0.927 r=0.803

At 500 pg input RNA, WT Pico Kit has higher signal and fold change correlation with 50 ng RNA than target preparation methods from other suppliers, showing superior performance of WT Pico Kit.

MicroArray Quality Control Sample A (MAQC A) from Agilent Technologies and MAQC B from Ambion™, Thermo Fisher Scientific were prepared using WT Pico Kit and WT PLUS Kit and analyzed on transcriptome profiling arrays from Affymetrix.

The ratio of gene-level expression of MAQC A/B at 500 pg prepared with WT Pico Kit and Company N was compared with 50 ng prepared using WT PLUS Kit.

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WT Pico Kit processes samples as low as 100 pg better than other suppliers

MAQC A signal MAQC B signal MAQC A/Bfold change

WT

Pic

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it1

00

pg

Co

mp

an

y N

10

0 p

g

50 ng RNA WT PLUS Kit

r=0.942 r=0.931 r=0.827

r=0.903 r=0.895 r=0.661

MicroArray Quality Control Sample A (MAQC A) from Agilent Technologies and MAQC B from Ambion™, Thermo Fisher Scientific were prepared using WT Pico Kit and WT PLUS Kit and analyzed on transcriptome profiling arrays from Affymetrix.

The ratio of gene-level expression of MAQC A/B at 100 pg prepared with WT Pico Kit and Company N was compared with 50 ng prepared usingWT PLUS Kit.

At 100 pg input RNA, WT Pico Kit has higher signal and fold change correlation with 50 ng RNA than target preparation methods from other suppliers, showing superior performance of WT Pico Kit.

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WT Pico Kit detects ~4x more genes with significant fold changes than other suppliers

This volcano plot shows WT Pico Kit (Blue) overlaid with another supplier, Company N (Red) at 500 pg RNA input.

Fold change is plotted on the x-axis and significance is plotted on the y-axis.

The blue signal on the volcano plot indicates detection of nearly 4x greater genes with significant fold change differences using WT Pico Kit versus Company N.

The points shaded in grey show data below the chosen fold change and/or significance cut offs.

Data is displayed in Transcriptome Analysis Console (TAC) Software from Affymetrix.

Number of genes

WT Pico Kit: 8,834

Company N: 2,244

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NEW Clariom™ solutions for limited samples

Prepare

Detect

3.

4. 1.

2.

Analyze

Interpret

Learn more at www.affymetrix.com/pico

Single kit for key sample types including FFPE, blood, and fresh tissue

GeneChip® WT Pico Kitfor as little as 100 pg RNA

Clariom™ D arrays for human, mouse, and rat

Get the broadest view of the transcriptome by measuring gene-level, transcript-level of protein-coding, or non-coding RNA

Transciptome Analysis Console (TAC) Software

Transcriptome profiling and alternative splicing analysis for biologists in minutes

Expression Console™ Software

Simple data normalization and summarization

© 2016 Affymetrix, Inc. All rights reserved. For Research Use Only. Not for use in diagnostic procedures