Comment[ArrayExpressAccession]	E-GEOD-39229
MAGE-TAB Version	1.1							
Public Release Date	2013-03-25
Investigation Title	Mapping Epigenomic Type-Specific Differences Occurring During Hematopoiesis							
Comment[Submitted Name]	Mapping Epigenomic Type-Specific Differences Occurring During Hematopoiesis
Experiment Description	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. Refer to individual Series.							
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl						
Person Last Name	Abraham	Abraham	Cui	Tang	Zhao			
Person First Name	Brian	Brian	Kairong	Qingsong	Keji			
Person Mid Initials	J	J						
Person Email	geo@ncbi.nlm.nih.gov							
Person Affiliation	NHLBI - Lab of Molecular Immunology							
Person Address	NHLBI - Lab of Molecular Immunology, 10 Center Drive; Bldg 10; Rm 7B20, Bethesda, MD, USA							
Person Roles	submitter							
Protocol Name	P-GSE39229-6	P-GSE39229-8	P-GSE39229-7	P-GSE39229-2	P-GSE39229-4	P-GSE39229-1	P-GSE39229-3	P-GSE39229-5
Protocol Description	Treated as described in SRP000801. To examine the changes of chromatin modifications before and after differentiation, we fragmented the chromatin from CD133+ cells using micrococcal nuclease (MNase) digestion and performed ChIP-Seq analysis as described previously (Barski et al., 2007 A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev and K. Zhao, High-resolution profiling of histone methylations in the human genome, Cell 129 (2007), pp. 823-837. As described in Barski et al., 2007 (A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev and K. Zhao, High-resolution profiling of histone methylations in the human genome, Cell 129 (2007), pp. 823-837).	Purified from whole blood using human Naive B cell isolation kit II kits (Miltenvi #130-091-150) As described in Barski et al., 2007 (A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev and K. Zhao, High-resolution profiling of histone methylations in the human genome, Cell 129 (2007), pp. 823-837).	Treated as described in SRP000801. To examine the changes of chromatin modifications before and after differentiation, we fragmented the chromatin from CD36+ cells using micrococcal nuclease (MNase) digestion and performed ChIP-Seq analysis as described previously (Barski et al., 2007 A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev and K. Zhao, High-resolution profiling of histone methylations in the human genome, Cell 129 (2007), pp. 823-837. As described in Barski et al., 2007 (A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev and K. Zhao, High-resolution profiling of histone methylations in the human genome, Cell 129 (2007), pp. 823-837).	As in Chepelev et al, Nucleic Acids Research, 2009.	CD4 cells isolated and treated as in SRP000201. CD4+ T cells were purified from human blood using human CD4+ T cell isolation kit II kits (Miltenyi). The cells were digested with MNase to generate mainly mononucleosomes with minor fraction of dinucleosomes for histone modification mapping. For mapping enzyme target sites, the cells were crosslinked with formaldehyde treatment and chromatin fragmented to 200 to 300 bp by sonication. Chromatin from 2.0E+7 cells was used for each ChIP experiment, which yielded approximately 200 ng of DNA. The ChIP DNA ends were repaired using PNK and Klenow enzyme, followed by treatment with Taq polymerase to generate a protruding 3' A base used for adaptor ligation. Following ligation of a pair of Solexa adaptors to the repaired ends, the ChIP DNA was amplified using the adaptor primers for 17 cycles and the fragments around 220 bp (mononucleosome + adaptors) isolated from agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Solexa 1G Genome Analyzer following manufacturer protocols. As described in Barski et al., 2007 (A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev and K. Zhao, High-resolution profiling of histone methylations in the human genome, Cell 129 (2007), pp. 823-837).	N/A	Illumina Casava1.7 software used for basecalling. Reads were aligned using TopHat 1.3.1 on top of Bowtie 0.12.7 to the hg18 genome with default parameters accepted_hits file was converted to BED using SAMtools. For graph-making and RPKM calculations, and all subsequent analyses, chromosome Y reads were discarded as some sources in study were female. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Hu et al 2011. Briefly reads in RefSeq gene exons were counted and normalized by total genic exon size and library size. Genome_build: hg18 Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample with columns: RefSeq ID, RPKM, exon base pair count, read count, unique ID, num genes w/ ID Supplementary_files_format_and_content: BED file of TopHat mapped reads	Illumina Casava1.7 software used for basecalling. Reads mapped to hg18 using bowtie 0.12.7, with -m 1 allowing one location per read Mapped reads filtered to allow one read per position Pol II and p300 binding sites calculated using MACS 1.4.1, -s hg, --p-value=1e-8 H2AZ analyzed with SICER using -w 200 -g 400 -t 0.68 -e 100 -f 150 -p 1e-5 H3K4 analyzed with SICER using -w 200 -g 200 -t 0.68 -e 100 -f 150 -p 1e-5 Brg1 analyzed with SICER using -w 200 -g 600 -t 0.68 -e 100 -f 150 -p 1e-5 H3K27 analyzed with SICER using predicted -w -I 150 -t 0.68 -e 100 -g 0 -f 150 -p 1e-5, Outermost windows of H3K27 islands were trimmed to maximize the difference between island and non-island bins of 50bp Genome_build: hg18 Supplementary_files_format_and_content: BED: chromosome, start, end, ReadID, number of mapping locations of read, strand Supplementary_files_format_and_content: Island: chromosome, start, end, reads in island in control, reads in island in test, pvalue, normalized fold change, FDR Supplementary_files_format_and_content: bsites (Peak): chromosome, start, end, peak ID, -10(log10(pvalue))
Protocol Type	nucleic acid library construction protocol	nucleic acid library construction protocol	nucleic acid library construction protocol	nucleic acid library construction protocol	nucleic acid library construction protocol	grow	feature_extraction	feature_extraction
Experimental Factor Name	CELL TYPE	CHIP ANTIBODY DETAILS						
Experimental Factor Type	cell type	chip antibody details						
Comment[SecondaryAccession]	GSE39229							
Comment[GEOReleaseDate]	2013-03-25							
Comment[ArrayExpressSubmissionDate]	2012-07-10							
Comment[GEOLastUpdateDate]	2013-03-25							
Comment[AEExperimentType]	RNA-seq of coding RNA							
Comment[AEExperimentType]	ChIP-seq							
SDRF File	E-GEOD-39229.sdrf.txt