E-GEOD-6506 - Transcription profiling of human hematopoietic stem cells vs. differentiated progeny

Status
Submitted on 11 December 2006, released on 14 June 2008, last updated on 10 June 2011
Organism
Mus musculus
Samples (20)
Array (1)
Protocols (4)
Description
Hematopoietic stem cells (HSC) continuously regenerate a complete hematologic and immune system. Very few genes that regulate this process have yet been identified. In order to identify factors governing differentiation, we have compared the transcriptome of highly purified HSC with their differentiated progeny, including erythrocytes, granulocytes, monocytes, NK cells, activated and naïve T-cells, and B-cells. Chromosomal analysis revealed that HSC were more transcriptionally active than other cell types across most chromosomes. Each lineage expressed ~100 to 400 genes uniquely, including many previously uncharacterized genes. Overexpression of two fingerprint genes resulted in a significant bias in differentiation indicating a role in cell fate determination, demonstrating the utility of these data for modulation of specific cell types. Experiment Overall Design: Goal - Expression profiling of hematopoietic cells Experiment Overall Design: Description - Biological replicates of 10 hematopoietic cell types from female C57Bl/6 mice were purified for microarray analysis Experiment Overall Design: Experimental Factors: wild-type female C57Bl/6 CD45.1 Mus musculus Experiment Overall Design: Experimental Design: 25,000- 50,000 cells were FACS sorted, mRNA was purified by RNAqueous (Ambion), DNAse treated with DNAse1, phenol:chloroform:isoamyl alcohol extracted, and amplified through two rounds of in vitro transcription using MessageAmp (Ambion). Second round was biotinylated with bio-CTP and bio-UTP. Experiment Overall Design: Microarrays: Oligonucleotide, Affymetrix, Moe430 v 2.0 Experiment Overall Design: QC: Biological replicates, correlation coefficient > .95; scale factor <10; 5'/3' ratio < 20
Experiment types
transcription profiling by array, unknown experiment type
Contact
Nathan C. Boles
Citation
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-6506.idf.txt
Sample and data relationshipE-GEOD-6506.sdrf.txt
Raw data (1)E-GEOD-6506.raw.1.zip
Processed data (1)E-GEOD-6506.processed.1.zip
Array designA-AFFY-45.adf.txt
R ExpressionSetE-GEOD-6506.eSet.r
Links