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Sample GSM4301068 Query DataSets for GSM4301068
Status Public on Sep 30, 2020
Title MCF7_ARID1B_E2_Chipseq
Sample type SRA
Source name breast cancer cells
Organism Homo sapiens
Characteristics cell line: MCF7
treatment: E2 (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
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
BioSample SAMN14056039
SRA SRX7692225

Supplementary file Size Download File type/resource 163.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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