|
| Status |
Public on Sep 04, 2020 |
| Title |
BT549-PTEN-PolII-Rep2 (control) |
| Sample type |
SRA |
| |
|
| Source name |
Breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BT-549
genotype: PTEN over-expressed
treatment: control
chip antibody: Rpb1 (D8L4Y) (Cell Signaling cat# 14958)
|
| Treatment protocol |
Three hours of glucose deprivation
|
| Growth protocol |
Cells were cultured in DMEM/F-12 medium (Life Technologies, Grand Island, NY) supplemented with 10% FBS (Thermo Scientific Gibco, Waltham, MA) at 37°C with 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was immunoprecipitated using RNA Pol II antibody, washed, reverse-crosslinked, and DNA isolated using the phenol-chloroform method. Input DNA isolated using the phenol-chloroform method
10ng precipitated DNA was used to prepare library using Illumina TruSeq ChIP library preparation kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Base calling and generation of FASTQ files performed using standard CASAVA pipeline
Reads were aligned against hg38 by using Bowtie2.
BAM files were normalized by depth after removal of PCR duplicates and blacklisted regions.
For generating heatmap and metagene plots, ngs.plot program was used.
Genome_build: hg38
Supplementary_files_format_and_content: Library normalized bigWig files were provided.
|
| |
|
| Submission date |
Jun 17, 2020 |
| Last update date |
Sep 04, 2020 |
| Contact name |
Ata Abbas |
| E-mail(s) |
[email protected]
|
| Organization name |
Case Western Reserve University
|
| Department |
Division of Hematology & Oncology
|
| Street address |
10900 Euclid Ave
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE152559 |
PTEN-dependent regulation of genome-wide transcription during metabolic stress [ChIP-Seq] |
| GSE152602 |
PTEN-dependent regulation of genome-wide transcription during metabolic stress |
|
| Relations |
| Reanalysis of |
GSM3538830 |
| BioSample |
SAMN15295627 |
| SRA |
SRX8564014 |
