|
| 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.
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| |
|
| 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.
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| |
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| 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 |
| E-mail(s) |
agardini@wistar.org
|
| 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)
|
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| This SubSeries is part of SuperSeries: |
| GSE45715 |
Genome-wide analysis of BRCA1 and PALB2 |
|
| Relations |
| BioProject |
PRJNA174355 |
| SRA |
SRP015361 |
| 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 Selector |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
| Raw data are available in SRA |
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