|
| Status |
Public on Feb 22, 2016 |
| Title |
RUNX1 ChIP-seq replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
MCF7 cells
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: RUNX1
antibody vendor/catalog#: ab23980, Abcam
|
| Treatment protocol |
G1/S cell cycle synchronization was achieved by double-thymidine block. Cells were incubated for 16 h in media containing 2 mM thymidine (Sigma-Aldrich), released for 8-12 h in DMEM containing 10% FBS, and then incubated again in 2 mM thymidine for 16-18 h. For G2/M synchronization, cells were released from the double-thymidine block for 4 hours prior to treatment with 100 nM nocodazole (Sigma-Aldrich) for 14h. Percentage of cells in the various phases of the cell cycle were quantitated by propidium iodide staining and flow cytometry using BD LSRII flow cytometer (BD Biosciences) and the Modfit LT SynchWizard Tool (Verity Software House).
|
| Growth protocol |
MCF7 BCa cells from the American Type Culture Collection were cultured in DMEM (Mediatech, Inc.) supplemented with 10% FBS (Gemini Bio-products). The MCF7/shRx1RUNTdox and MCF7/shRx13’UTRdox sublines were created by transducing MCF7 cells with pSLIK-based lentiviruses engineered as previously described (Baniwal et al. 2010) to conditionally express shRNAs that target either the RUNT domain or the 3’UTR of RUNX1, respectively. Transduced cells were selected with 2 mg/ml Neomycin (Gemini Bio-products).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared according to Illumina protocols for DNA samples
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ChIP-seq library for RUNX1 in MCF7 cells
|
| Data processing |
Reads passing quality filtering were aligned to the hg19 build of the human genome with bowtie2 (Langmead and Saslzberg 2012).
Peak finding was performed with MACS (Zhang et al., Genome Bio 2009) with a p-value threshold of 1e-5. Only peaks identified in both replicates were considered for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bed files containing coordinates of peaks
|
| |
|
| Submission date |
Jan 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Dustin E Schones |
| E-mail(s) |
dschones@coh.org
|
| Organization name |
City of Hope
|
| Street address |
1500 E Duarte Rd.
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE65313 |
Breast Cancer Suppressor Role of RUNX1: Estrogen-dependent Regulation of AXIN1 and b-catenin |
|
| Relations |
| BioSample |
SAMN03295089 |
| SRA |
SRX852986 |
