|
| Status |
Public on Oct 30, 2020 |
| Title |
YCC11_EBF1 |
| Sample type |
SRA |
| |
|
| Source name |
gastric cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: YCC11
cell type: gastric cancer cell line
chip antibody: EBF1 (Santa Cruz Biotechnology, sc-137065)
|
| Treatment protocol |
EBF1 cDNAs were cloned into MIGR1 vector (#27490, Addgene) between the HpaI and Bgl 2 sites. Retrovirus packaging was performed using Platinum-A (Plat-A) retroviral packaging cell lines by transfection using Lipofectamin 2000 (Thermo Fisher Scientific). GC cells were infected with retrovirus packaged with EBF1 genes for 48 hours and sorted for GFP.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
30 million cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and reactions were stopped by adding glycine to a final concentration of 0.2 M. Chromatin was extracted and sonicated to 500 bp. EBF1 (sc-137065, Santa Cruz Biotechnology; H00001879-M01, Abnova) and EZH2 (#5246, Cell Signaling) antibodies were used for chromatin immunoprecipitation (ChIP). Input DNA from cells prior to immunoprecipitation were used to normalize ChIP-seq peak calling.
ChIPed DNA (10 ng) was used for ChIP with DNA sequencing (ChIP-seq) library construction following manufacturer protocols (New England Biolabs).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
EBF1 ChIP-seq in YCC11
|
| Data processing |
Sequencing reads were mapped to the human reference genome (hg19) using BWA-MEM. Reads with MAPQ<10 and potential PCR duplication were filtered using SAMTools. Peaks were predicted using MACS2 with default parameters.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_peaks.txt: Please refer to the website: https://github.com/taoliu/MACS for details.
|
| |
|
| Submission date |
Oct 18, 2018 |
| Last update date |
Oct 30, 2020 |
| Contact name |
Wen Fong Ooi |
| E-mail(s) |
[email protected]
|
| Organization name |
Genome Institute of Singapore
|
| Street address |
60 Biopolis
|
| City |
Singapore |
| ZIP/Postal code |
470110 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE121140 |
Genomic and Epigenomic EBF1 Alterations Modulate TERT Expression in Gastric Cancer |
| GSE121495 |
Genomic and Epigenomic EBF1 Alterations Modulate TERT Expression in Gastric Cancer [ChIP-Seq - EBF1, EZH2] |
|
| Relations |
| BioSample |
SAMN10258624 |
| SRA |
SRX4905629 |
