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Series GSE67892 Query DataSets for GSE67892
Status Public on Jun 28, 2016
Title CTCF and CohesinSA-1 Mark Active Promoters and Boundaries of Repressive Chromatin Domains in Primary Human Erythroid Cells [RNA-Seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary CTCF and cohesinSA-1 are regulatory proteins involved in a number of critical cellular processes including transcription, maintenance of chromatin domain architecture, and insulator function. To assess changes in the CTCF and cohesinSA-1 interactomes during erythropoiesis, chromatin immunoprecipitation coupled with high throughput sequencing and mRNA transcriptome analyses via RNA-seq were performed in primary human HSPC hematopoietic stem and progenitor cells (HSPC) and primary human erythroid cells from single donors. Sites of CTCF and cohesinSA-1 co-occupancy were enriched in gene promoters in HSPC and erythroid cells compared to single CTCF or cohesin sites. Cell type-specific CTCF sites in erythroid cells were linked to highly expressed genes, with the opposite pattern observed in HSPCs. Chromatin domains were identified by ChIP-seq with antibodies against trimethylated lysine 27 histone 3, a modification associated with repressive chromatin. Repressive chromatin domains increased in both number and size during hematopoiesis, with many more repressive domains in erythroid cells than HSPCs. CTCF and cohesinSA-1 marked the boundaries of these repressive chromatin domains in a cell-type specific manner. These genomic data support the hypothesis that CTCF and cohesinSA-1 have multiple roles in the regulation of gene expression during erythropoiesis including transcriptional regulation at gene promoters and maintenance of chromatin architecture.
 
Overall design CD34+-selected stem and progenitor cells were expanded for three days in the absence of EPO. The cells were further cultured in the presence of EPO, and cells differentiated into R3/R4 nucleated erythroid cells. RNA was isolated from three biological replicates of each cell type and sequencing libraries were prepared from poly A selected RNA.
 
Contributor(s) Steiner LA, Schulz VP, Maksimova Y, Lezon-Geyda K, Gallagher PG
Citation(s) 27219007
Submission date Apr 14, 2015
Last update date May 15, 2019
Contact name Vince Schulz
E-mail(s) vincent.schulz@yale.edu
Organization name Yale University
Department Department of Pediatrics
Lab Gallagher
Street address 333 Cedar St. LMP 4085
City New Haven
State/province CT
ZIP/Postal code 06519
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (6)
GSM1657637 HSPC_rep1
GSM1657638 HSPC_rep2
GSM1657639 HSPC_rep3
This SubSeries is part of SuperSeries:
GSE67893 CTCF and CohesinSA-1 Mark Active Promoters and Boundaries of Repressive Chromatin Domains in Primary Human Erythroid Cells
Relations
BioProject PRJNA281131
SRA SRP057177

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

Supplementary file Size Download File type/resource
GSE67892_ReadCounts_RNAseq.txt.gz 253.5 Kb (ftp)(http) TXT
GSE67892_log2RPKM_RNAseq.txt.gz 1021.3 Kb (ftp)(http) TXT
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Processed data are available on Series record
Raw data are available in SRA

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