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Signatures of Proliferation and Quiescence in Hematopoetic Stem Cells

T. Venezia, A. Merchant, C. Ramos, N. Whitehouse, A. Young, C. Shaw and M. Goodell

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Experimental Description

This study utilizes Affymetrix MGU74Av2 microarrays to investigate signatures of proliferation and quiescence in hematopoetic stem cells (HSC). The experimental design consists of 2 arms: (1) a time course of microarrays performed on adult hematopoetic stem cells (SP cells) after treatment with 5-fluorouracil; and (2) an analysis of fetal liver derived HSC in comparison with untreated adult HSC. Microarray data from both arms of the experiment are available for download through this site.

QC Selection

Quality control parameters were used to select the arrays analyzed in this study. The QC values for each array are shown in the table below. The single chip QC criterion is: scale factor (affy) < 10, Perfect Match median intensity > 100, b-actin 3'-5' ratio < 25, R^2 > 0.97 for replicate arrays. (see paper for details). Individual microarrays had to meet all of these criteria in order to be included in the study.

Normalization and Data Processing

Normalization and expression modeling were performed in the R open source statistical computing environment, with extensive use of the Bioconductor suite of R packages (see Bioconductor.org). In particular, probe level summaries were computed using the GC-RMA method (see the paper for reference). The GCRMA normalized data for each treatment and for the entire study are available for download through this site.

Data for Download

Click a link to download data for each format for the entire collection of arrays (16 arrays).

  • Windows users should download the zip files.
  • Mac OSX/Linux/Unix users should download the tar.gz files.
DAT files (450MB): Affymetrix raw image file format. All DAT: gzip, zip
CEL files (43 MB): Affymetrix quantitation file format. All CEL (probe level data): gzip, zip
GCRMA files (1.6 MB): GC-RMA Normalized data. (see Bioconductor.org) All GCRMA: XLS (MS Excel)

Treatment Data Download Replicate name Scale factor PM median intensity b-actin 3'5' ratio R2 of replicates Technical Information
Adult HSC day 0 (untreated SP cells)
SP0-1
5.7
135.3
5.8
0.98
Download
SP0-2
4.7
187.0
13.4

Adult HSC day 1 (5FU treated)
SP1-1
2.3
247.0
15.0
0.99
Download
SP1-2
2.3
277.0
10.5

Adult HSC day 2 (5FU treated)
SP2-1
3.8
185.5
7.4
0.99
Download
SP2-2
3.1
213.8
7.2

Adult HSC day 3 (5FU treated)
SP3-1
4.2
248.8
16.1
0.98
Download
SP3-2
6.2
178.0
10.9

Adult HSC day 6 (5FU treated)
SP6-1
4.9
155.0
3.4
0.98
Download
SP6-2
3.2
244.3
5.1

Adult HSC day 10 (5FU treated)
SP10-1
5.3
190.5
24.2
0.98
Download
SP10-2
7.0
131.3
16.0

Adult HSC day 30 (5FU treated)
SP30-1
6.4
174.0
12.3
0.97
Download
SP30-2
5.9
139.3
19.8

FL-HSC (untreated FL HSC cells)
fetal liver KLS-1
5.8
145.0
2.5
0.97
Download
fetal liver KLS-2
9.4
109.3
6.3

 

       
   
             
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