|
| Status |
Public on May 18, 2020 |
| Title |
MCF7_GATA3_Chipseq |
| Sample type |
SRA |
| |
|
| Source name |
breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
growth protocol: control (parental cell)
growth medium: Full media
chip antibody: GATA3 (Cell Signaling, CST5852)
|
| Treatment protocol |
For knockdown of GATA3 or JUN, MCF7 parental or TamR cells were infected with shRNA lentiviruses and selected by puromycin (1 μg/ml) for 3 days to establish GATA3 knockdown MCF7 parental or JUN knockdown TamR stable cell lines. For the Dox-inducible GATA3, JUN-overexpressing cell lines, GATA3 and JUN cDNAs (Open Biosystems) were cloned into the pInducer 20 destination vector (Meerbrey et al., 2011) using the Gateway system (Invitrogen). Lentivirus was produced in 293T cells and used to infect cells in media containing polybrene (8 μg/ml). Cells were selected for 4 days by 500 μg/mL G418 (Invitrogen) after virus infection to get inducible overexperssion stable lines. To induce GATA3 or JUN protein expression, 1 μg/ml doxycycline was added into culture media for about 48 h before collection for experiments. For knockdown of GATA3 and overexpression of JUN in MCF7 parental cells at the same time, Dox-inducible JUN-overexpressing MCF7 parental stable cell line was further infected with shGATA3 lentiviruses and selected by puromycin (1 μg/ml) for 24 h, then 1 μg/ml doxycycline was added into culture media to induce JUN overexpression for about 48 h before collection for experiments.
|
| Growth protocol |
MCF7 parental cells were maintained in RPMI/1640 supplemented with 10% heat-inactivated FBS (Sigma) and 1% penicillin-streptomycin (P/S). The TamR cells were kept in phenol-red free RPMI/1640 medium supplemented with 10% heat-inactivated charcoal-stripped-FBS and 1% P/S with the addition of 100 nM 4-hydroxytamoxifen (4-OHT, H7904, Sigma). All cells were kept at 37 °C in a humified incubator with 5% CO2.
|
| 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 LTP Library Preparation Kit (KK8230) or 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 |
Mar 18, 2019 |
| Last update date |
May 19, 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) |
| GSE128445 |
Enhancer reprogramming driven by high-order assemblies of transcription factors promotes phenotypic plasticity and breast cancer endocrine resistance [ChIP-Seq] |
| GSE128460 |
Enhancer reprogramming driven by high-order assemblies of transcription factors promotes phenotypic plasticity and breast cancer endocrine resistance |
|
| Relations |
| BioSample |
SAMN11159164 |
| SRA |
SRX5534865 |
