|
| Status |
Public on Sep 30, 2020 |
| Title |
MCF7_ARID1B_Veh_Chipseq |
| Sample type |
SRA |
| |
|
| Source name |
breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
treatment: Vehicle (one hour)
chip antibody: ARID1B(Bethyl, A301-046A)
|
| Treatment protocol |
Before experiment, the MCF7 cells were hormone-stripped in phenol red-free DMEM medium plus 5% charcoal-treated FBS for 3 days, followed by treatemnt of either 100 nM 17β-estrodial (E2) or ethanol as vehcile control for 1hr.
|
| Growth protocol |
MCF7 obtained from ATCC were cultured in DMEM media supplemented with 10% FBS in a 5% CO2 humidified incubator at 37°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The extracted ChIP DNA was ligated to specific adaptors using KAPA Hyper Prep Kit (KK8504), according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Basecalls performed using Illuminal CASAVA software.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie v1.1.2 with only uniquely mapped reads retained.
Peaks were called using MACS2 with q-value less than 1e-5. The peaks overlapped with the blacklist regions downloaded from UCSC were removed
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file
|
| |
|
| Submission date |
Feb 07, 2020 |
| Last update date |
Oct 01, 2020 |
| Contact name |
Zhijie Jason Liu |
| E-mail(s) |
liuz7@uthscsa.edu
|
| Organization name |
Universality of Texas Health Science Center at San Antonio
|
| Department |
Department of Molecular Medicine
|
| Lab |
Liu lab
|
| Street address |
7703 Floyd Curl Drive
|
| City |
San Antonio |
| State/province |
TEXAS |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE144926 |
Epigenomics-Based Identification of Estrogen-regulated Long Noncoding RNAs in ER+ Breast Cancer [ChIP-Seq] |
| GSE144927 |
Epigenomics-Based Identification of Estrogen-regulated Long Noncoding RNAs in ER+ Breast Cancer |
|
| Relations |
| BioSample |
SAMN14056041 |
| SRA |
SRX7692224 |
