SCGAP at Princeton and Penn
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Experiment Description:

This study is to determine global gene expression profiles for mouse and human hematopoietic stem cells and other stages of the hematopoietic hierarchy. The experiments were performed based on Affymetrix HG-U95 and MG-U74 v2 sets. The data were generated in Lemischk's group at Princeton University.

CEL files are available via ftp download. Please call (215) 746-7016 to obtain the login and password to access the data.

Sample Array Total # of Probe Sets # of Expressed Probe Sets* FDR Summary Link
mouse adult bone marrow long-term hematopoietic stem cells MG-U74Av2 12488 2956 0.01 details probe sets
MG-U74Bv2 12477 463 0.01 details probe sets
MG-U74Cv2 11934 183 0.02 details probe sets
mouse adult bone marrow short-term hematopoietic stem cells MG-U74Av2 12488 3345 0.01 details probe sets
MG-U74Bv2 12477 411 0.01 details probe sets
MG-U74Cv2 11934 317 0.02 details probe sets
mouse adult bone marrow lineage-committed progenitors MG-U74Av2 12488 2297 0.01 details probe sets
MG-U74Bv2 12477 1179 0.01 details probe sets
MG-U74Cv2 11934 143 0.02 details probe sets
mouse adult bone marrow mature blood cells MG-U74Av2 12488 2065 0.01 details probe sets
MG-U74Bv2 12477 1362 0.02 details probe sets
MG-U74Cv2 11934 397 0.05 details probe sets
mouse fetal liver hematopoietic stem cells MG-U74Av2 12488 2693 0.01 details probe sets
MG-U74Bv2 12477 1465 0.02 details probe sets
MG-U74Cv2 11934 506 0.05 details probe sets
mouse fetal liver lineage-committed progenitors MG-U74Av2 12488 3705 0.01 details probe sets
MG-U74Bv2 12477 2387 0.02 details probe sets
MG-U74Cv2 11934 384 0.05 details probe sets
mouse fetal liver mature blood cells MG-U74Av2 12488 2712 0.01 details probe sets
MG-U74Bv2 12477 681 0.02 details probe sets
MG-U74Cv2 11934 288 0.05 details probe sets
human fetal liver hematopoietic stem cells HG-U95Av2 12626 3810 0.01 details probe sets
HG-U95B 12620 2867 0.01 details probe sets
HG-U95C 12646 1562 0.01 details probe sets
HG-U95D 12644 490 0.05 details probe sets
HG-U95E 12639 1181 0.05 details probe sets
human fetal liver lineage-committed progenitors HG-U95Av2 12626 4064 0.01 details probe sets
HG-U95B 12620 2731 0.01 details probe sets
HG-U95C 12646 1525 0.01 details probe sets
HG-U95D 12644 436 0.05 details probe sets
HG-U95E 12639 1247 0.05 details probe sets
human fetal liver mature blood cells HG-U95Av2 12626 4168 0.01 details probe sets
HG-U95B 12620 3319 0.01 details probe sets
HG-U95C 12646 1594 0.01 details probe sets
HG-U95D 12644 650 0.05 details probe sets
HG-U95E 12639 1343 0.05 details probe sets
Method: The significance test of presence or absence of probe sets was adjusted for the multiple testing problem. Here we used the approach of controlling the False Discovery Rate (FDR) rate. Specifically, for each asssay, the p-values of absolute expression analysis of probe sets from Affymetrix MAS 5.0 were adjusted using Benjamini-Hochberg step-up FDR method, the probe set is then called "Present" if the adjusted p-value is less than the specified FDR, otherwise called "Absent". If there are more than one assay for a population, the probe set is called "Present" if it is called "Present" in more than half of the assays for that population.
*Note: This number does not include the 66 controls on each array.