|
| Status |
Public on Jun 23, 2020 |
| Title |
MCF7, WT_ER_Veh (ChIP-Seq) |
| Sample type |
SRA |
| |
|
| Source name |
MCF7
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
transfection: WT ER
treatment: Veh
chip antibody: HA (Thermofisher, 88837)
|
| Treatment protocol |
For MCF7 cells with different ER truncations, MCF7 cells were first infected with lentivirus-based ER truncations, and then transiently infected shER targeting 3'UTR to knock down endogenous ER. Cells were kept in hormone stripped condition for at least three days before treating with 100 nM estradiol or corresponding condition of ethanol for 30 min.ER_pbox/WT ChIP was done in full medium condition.
|
| 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 or by HA antibody conjugated magnet beads pull-down.
The extracted ChIP DNA was ligated to specific adaptors of ThruPLEX DNA-seq kit (R400427), according to the manufacturer’s instructions.ER_pbox/WT ChIP library was constructed by KAPA Hyper Prep system (KK8504)
|
| |
|
| 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 |
Aug 03, 2019 |
| Last update date |
Jun 24, 2020 |
| Contact name |
Kexin Xu |
| Organization name |
UT Health Science Center at San Antonio
|
| Department |
Molecular Medicine
|
| Street address |
7703 Floyd Curl, MC 8257
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE135340 |
Enhancer RNA mediate estrogen-induced transcriptional repression by recruiting ERa and its cofactor to selective enhancers [ChIP-Seq] |
| GSE135341 |
Enhancer RNAs mediate estrogen-induced decommissioning of selective enhancers by recruiting ER and its cofactor |
|
| Relations |
| BioSample |
SAMN12491202 |
