|
| Status |
Public on Jun 11, 2020 |
| Title |
Reduced representation bisulfite sequencing (RRBS) of breast cancer cell lines |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
Breast cancers can be divided into subtypes with different prognoses and treatment responses based on global gene expression differences. This study utilized integrated analysis of DNA methylation, chromatin accessibility, transcription factor binding, and gene expression in large collections of breast cancer cell lines and patient tumors to identify transcription factors responsible for the basal-like gene expression program. The results of this study indicate that glucocorticoid receptor (GR) and signal transducer and activator of transcription 3 (STAT3) bind to the same genomic regulatory regions that are specifically open and unmethylated in basal-like breast cancer. These transcription factors cooperate to regulate expression of hundreds of genes in the basal-like gene expression signature and these downstream genes are associated with poor prognosis in patients.
|
| |
|
| Overall design |
To identify regulatory regions specific to basal-like breast cancer, reduced representation bisulfite sequencing (RRBS) was performed on 28 breast cancer cell lines (18 basal-like and 10 luminal) in order to measure DNA methylation across the genome.
|
| |
|
| Contributor(s) |
Varley K |
| Citation(s) |
32816914, 35221336 |
| |
| Submission date |
Jun 10, 2020 |
| Last update date |
Mar 30, 2022 |
| Contact name |
Katherine E Varley |
| E-mail(s) |
kt.varley@hci.utah.edu
|
| Organization name |
Huntsman Cancer Institute University of Utah
|
| Department |
Department of Oncological Sciences
|
| Lab |
Varley Lab
|
| Street address |
2000 Circle of Hope, Room 3719
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
|
| Samples (28)
|
|
| This SubSeries is part of SuperSeries: |
| GSE152205 |
Integrated analysis of DNA methylation, chromatin accessibility, transcription factor binding, and gene expression in large collections of breast cancer cell lines and patient tumors |
|
| Relations |
| BioProject |
PRJNA638632 |
| SRA |
SRP266790 |
Less...
More...