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Series GSE38788 Query DataSets for GSE38788
Status Public on Jun 10, 2015
Title Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [ChIP-Seq 1]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Basal-like and luminal breast tumors have distinct clinical behavior and molecular profiles, yet the underlying mechanisms are poorly defined. To interrogate processes that determine these distinct phenotypes and their inheritance pattern, we generated somatic cell fusions and performed integrated genetic and epigenetic (DNA methylation and chromatin) profiling. We found that the basal-like trait is generally dominant and it is largely defined by epigenetic repression of luminal transcription factors. Definition of super-enhancers highlighted a core program common in luminal cells but high degree of heterogeneity in basal-like breast cancers that correlates with clinical outcome. We also found that protein extracts of basal-like cells is sufficient to induce luminal-to-basal phenotypic switch implying a trigger of basal-like autoregulatory circuits. We determined that KDM6A might be required for luminal-basal fusions, and identified EN1, TBX18, and TCF4 as candidate transcriptional regulators of luminal-to-basal switch. Our findings highlight the remarkable epigenetic plasticity of breast cancer cells.
 
Overall design Examination of histone H3K27me3 modifications in 6 cell lines
 
Contributor(s) Polyak K, Maruyama R
Citation(s) 26051943
Submission date Jun 18, 2012
Last update date May 15, 2019
Contact name Kornelia Polyak
E-mail(s) kornelia_polyak@dfci.harvard.edu
Phone 617-632-2106
Organization name Dana-Farber Cancer Institute
Department Medical Oncology
Lab Polyak
Street address 450 Brookline Ave
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platforms (1)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Samples (6)
GSM949575 SUM159PT_H3K27me3_ChIPSeq
GSM949576 SUM159PT/T-47D_H3K27me3_ChIPSeq
GSM949577 SUM159PT/MCF7_H3K27me3_ChIPSeq
This SubSeries is part of SuperSeries:
GSE38548 Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer
Relations
SRA SRP013814
BioProject PRJNA170830

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

Supplementary file Size Download File type/resource
GSE38788_RAW.tar 657.0 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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