|Public on Sep 30, 2020
|breast cancer cells
|cell line: MCF7
treatment: Vehicle (one hour)
chip antibody: ARID1B(Bethyl, A301-046A)
|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.
|MCF7 obtained from ATCC were cultured in DMEM media supplemented with 10% FBS in a 5% CO2 humidified incubator at 37°C.
|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.
|Illumina HiSeq 3000
|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
Supplementary_files_format_and_content: bigWig file
|Feb 07, 2020
|Last update date
|Oct 01, 2020
|Zhijie Jason Liu
|Universality of Texas Health Science Center at San Antonio
|Department of Molecular Medicine
|7703 Floyd Curl Drive
|Epigenomics-Based Identification of Estrogen-regulated Long Noncoding RNAs in ER+ Breast Cancer [ChIP-Seq]
|Epigenomics-Based Identification of Estrogen-regulated Long Noncoding RNAs in ER+ Breast Cancer