|
| Status |
Public on Jun 04, 2019 |
| Title |
BT549-PTEN-PolII-Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
BT-549 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BT-549 (HTB-122)
treatment: PTEN over-expressed
chip antibody: Rpb1 (D8L4Y) (Cell Signaling cat# 14958)
|
| 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 for HiSeq runs.
Reads were aligned against hg19 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: hg19
Supplementary_files_format_and_content: Library normalized bigWig files (Rep1 and Rep2 merged) were provided.
|
| |
|
| Submission date |
Jan 04, 2019 |
| Last update date |
Dec 01, 2021 |
| 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) |
| GSE124657 |
PTEN modulates gene transcription by redistributing genome-wide RNA polymerase II occupancy [ChIP-seq] |
| GSE124659 |
PTEN modulates gene transcription by redistributing genome-wide RNA polymerase II occupancy |
|
| Relations |
| Reanalyzed by |
GSM4622800 |
| BioSample |
SAMN10691302 |
| SRA |
SRX5203072 |
