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Series GSE80728 Query DataSets for GSE80728
Status Public on Oct 10, 2016
Title Systematic identification of Ctr9 regulome in ERα-positive breast cancer
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Ctr9, the key scaffold subunit of the human RNA polymerase II (RNAPII) associated factor complex (PAFc), has been demonstrated as a positive regulator of ERα-positive breast cancer progression and ERα-target gene expression. Previously, we found that knockdown of Ctr9 reduces ERα protein stability and decreases the occupancy of ERα and RNAPII at select ERα-target genes. However, the genome-wide regulation of the occupancy of ERα and RNAPII mediated by Ctr9 is still unclear. Here, we determined the genome-wide ERα and RNAPII occupancy in response to estrogen induction and/or Ctr9 knockdown by performing chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq). We found that loss of Ctr9 dramatically decreases the global occupancy of ERα and RNAPII, highlighting the significance of Ctr9 in regulating estrogen signaling in ERα-positive breast cancer cells. Combining this resource with previously published genomic data sets, we identified a unique subset of ERα and Ctr9 target genes, and further delineates the possible independent function of Ctr9 from other subunits in PAFc.
 
Overall design ChIP-seq experiments for ERα and RNAPII
 
Contributor(s) Zeng H, Lu L, Zhong X, Xu W
Citation(s) 27829357
Submission date Apr 27, 2016
Last update date May 15, 2019
Contact name Xuehua Zhong
Organization name Wisconsin Institute for Discovery
Department Epigenetics
Street address 330 N. Orchard St.
City Madison
State/province WI
ZIP/Postal code 53705
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (12)
GSM2135485 Vehicle DMSO Input
GSM2135486 Vehicle E2 Input
GSM2135487 Dox DMSO Input
Relations
BioProject PRJNA319816
SRA SRP074073

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Supplementary file Size Download File type/resource
GSE80728_RAW.tar 2.6 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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