|
| Status |
Public on Jul 16, 2019 |
| Title |
MCF7_BLRP_TEAD4_MT_noDox_ChipSeq |
| Sample type |
SRA |
| |
|
| Source name |
MCF7
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
cell type: Breast cancer cell line
doxycycline: No Dox
treatment: Full medium
chip antibody: Biotin-ChIP using Streptavidin Magnetic beads (Solulink)
|
| Treatment protocol |
For knockdown of TEAD4 and YAP1, MCF7 cells were infected with shRNA lentiviruses and selected by puromycin (1 ug/ml) for 3 days to establish TEAD4 or YAP knockdown MCF7 stable cell lines. Before experiment, the MCF7 cells were hormone-stripped in phenol red-free DMEM medium plus 5% charcoal-treated FBS for 3 days, followed by treatment of either 100 nM 17β-estradiol (E2) or ethanol as vehicle control for 1hr. For knockdown of ERalpha in MCF7, at the second day of stripping, cells were treated with either 100 nM ICI182780 or DMSO for 24 hours before hormone treatment. To perform Biotin-ChIP experiments through Biotin-streptavidin pull-down, we used some BLRP-tagged MCF7 Tet-On inducible stable lines that can in vivo biotinylate BLRP-tagged proteins. To induce BLRP-tagged protein expression, 2 μg/ml doxycycline was added into culture media for about 24 hours before hormone treatment and collection.
|
| 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 streptavidin magnet beads pull-down.
The extracted ChIP DNA was ligated to specific adaptors of KAPA Hyper Prep system (KK8504), according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
MCF7_BLRP_TEAD4_MT_noDox
|
| Data processing |
Basecalls performed using Illumina 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 (GRCh37)
Supplementary_files_format_and_content: bigWig files
|
| |
|
| Submission date |
Jan 24, 2019 |
| Last update date |
Jul 16, 2019 |
| 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) |
| GSE125594 |
A non-canonical role of YAP/TEAD is required for activation of estrogen-regulated enhancers in breast cancer [ChIP-seq] |
| GSE125609 |
A non-canonical role of YAP/TEAD is required for activation of estrogen-regulated enhancers in breast cancer |
|
| Relations |
| BioSample |
SAMN10812930 |
| SRA |
SRX5287712 |
