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Series GSE40591 Query DataSets for GSE40591
Status Public on Sep 30, 2013
Title Genome-wide analysis of BRCA1 and PALB2 [ChIP-seq and RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Breast and ovarian cancer susceptibility genes, BRCA1 and PALB2 have enigmatic roles in cellular growth and mammalian development. While these genes are essential for growth during early developmental programs, inactivation later in adulthood leads to increased growth and formation of tumors, leading to their designation as tumor suppressors. We performed genome-wide analysis assessing their chromatin residence and gene expression responsiveness using high throughput sequencing in breast epithelial cells. These experiments revealed a critical role for BRCA1 and PALB2 in transcriptional responsiveness to NF-kB, a crucial mediator of growth and inflammatory response during development and cancer. Importantly, we also uncovered a vital role for these proteins in response to retinoic acid (RA), a growth inhibitory signal in breast cancer cells, which may constitute the basis for their tumor suppressor activity.
Overall design Comparison of the genome wide profiles of the BRCA protein complex (BRCA1 and PALB2) and phosphorylated RNAPII (P-Ser2) in MCF10A cells by ChIP-seq. Effect of BRCA1 and PALB2 knockdown (shRNAs) on transcription was assessed by RNA-seq.
Contributor(s) Gardini A, Cesaroni M, Shiekhattar R
Citation(s) 24591564
Submission date Sep 04, 2012
Last update date May 15, 2019
Contact name Alessandro Gardini
Phone 305-243-7394
Organization name University of Miami
Department Sylvester Comprehensive Cancer Center
Lab Ramin Shiekhattar
Street address 1501 NW 10 Avenue
City Miami
State/province FL
ZIP/Postal code 33136
Country USA
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (12)
GSM997540 BRCA1
GSM997541 PALB2
GSM997542 P-Ser2
This SubSeries is part of SuperSeries:
GSE45715 Genome-wide analysis of BRCA1 and PALB2
BioProject PRJNA174355
SRA SRP015361

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

Supplementary file Size Download File type/resource
GSE40591_BRCA1sh_Forward.wig.gz 275.9 Mb (ftp)(http) WIG
GSE40591_BRCA1sh_Reverse.wig.gz 273.9 Mb (ftp)(http) WIG
GSE40591_CTRLsh_Forward.wig.gz 369.0 Mb (ftp)(http) WIG
GSE40591_CTRLsh_Reverse.wig.gz 364.0 Mb (ftp)(http) WIG
GSE40591_PALB2sh_Forward.wig.gz 288.8 Mb (ftp)(http) WIG
GSE40591_PALB2sh_Reverse.wig.gz 285.9 Mb (ftp)(http) WIG
GSE40591_RAW.tar 967.4 Mb (http)(custom) TAR (of BEDGRAPH, BW, WIG)
GSE40591_RNAPolyA.bedGraph.gz 138.1 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

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