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Series GSE67783 Query DataSets for GSE67783
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 [ChIP-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy 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 formaldehyde crosslinked chromatin was isolated after cells differentiated into R3/R4 nucleated erythroid cells. Chromatin Immunoprecipitation followed by sequencing (chIP-seq) was performed using antibodies against CTCF, Cohesin SA1 and H3K27me3, along with a total input control. Two replicates for CTCF and Cohesin SA1 were obtained.
 
Contributor(s) Steiner LA, Schulz VP, Maksimova Y, Lezon-Geyda K, Gallagher PG
Citation(s) 27219007
Submission date Apr 12, 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. LCI401
City New Haven
State/province CT
ZIP/Postal code 06520-8064
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (12)
GSM1655735 HSPC_CTCF_1
GSM1655736 HSPC_SA1_1
GSM1655737 HSPC_H3K27me3
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 PRJNA281129
SRA SRP057176

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Supplementary file Size Download File type/resource
GSE67783_RAW.tar 13.2 Mb (http)(custom) TAR (of BED)
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Raw data are available in SRA
Processed data provided as supplementary file

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