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Series GSE39229 Query DataSets for GSE39229
Status Public on Mar 25, 2013
Title Mapping Epigenomic Type-Specific Differences Occurring During Hematopoiesis
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Formation of the blood from self-renewing hematopoietic stem cells to terminal lineages necessarily involves epigenomic modifications of the genome to control regulator and signature gene expression. By analysing the global expression profiles of hematopoietic stem cells (HSCs), in vivo differentiated CD4+ T cells and CD19+ B cells as well as in vitro differentiated erythrocyte precursor cells, we identified hundreds of transcripts showing type-specific expression in these cell types. To understand the epigenomic changes related to tissue-specific expression during HSC differentiation, we examined the genome-wide distribution of H3K4me1, H3K4me3, H3K27me1, H3K27me3, histone variant H2A.Z, chromatin remodeler BRG1, and RNA Polymerase II in the same four cell types, as well as embryonic stem cells. Analysis of these datasets revealed that numerous key differentiation genes are primed for expression by Brg1 and Pol II binding, as well as bivalent modifications in the HSCs prior to their expression in downstream differentiated cell types. Much of this bivalency in HSC is retained from embryonic stem cells. After differentiation, these modified regions resolve to active chromatin modification configuration in the specific lineage, while in parallel differentiated lineages the bivalent modification remains; Pol II and Brg1 are lost in closer lineages but bivalency resolves to silent monovalency in more distant lineages. Correlation of tissue-specific gene expression with the epigenomic changes predicts tens of thousands of potential common enhancers and tissue-specific enhancers, which may critically contribute to the expression patterns. We provide a valuable dataset for further understanding the regulatory mechanisms of differentiation and function of blood lineages.

This SuperSeries is composed of the SubSeries listed below.
Overall design Refer to individual Series.
Contributor(s) Abraham BJ, Cui K, Tang Q, Zhao K
Citation(s) 23510235
Submission date Jul 10, 2012
Last update date May 15, 2019
Contact name Brian J Abraham
Organization name St. Jude Children's Research Hospital
Department Computational Biology
Street address 262 Danny Thomas Blvd
City Memphis
State/province TN
ZIP/Postal code 38112
Country USA
Platforms (1)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
Samples (14)
GSM971331 B cell polyA RNA-Seq
GSM971332 CD4_Brg1
GSM971333 HSC_Brg1
This SuperSeries is composed of the following SubSeries:
GSE39537 Mapping Epigenomic Type-Specific Differences Occurring During Hematopoiesis [RNA-Seq]
GSE39538 Mapping Epigenomic Type-Specific Differences Occurring During Hematopoiesis [ChIP-Seq]
BioProject PRJNA171066

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE39229_RAW.tar 1.9 Gb (http)(custom) TAR (of BED, RPKM, TXT)
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