|
| Status |
Public on May 18, 2015 |
| Title |
H2AXpS139-ChIP-seq 6 h H.pylori rep2 |
| Sample type |
SRA |
| |
|
| Source name |
AGS cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: gastric cancer cell line
cell line: AGS
treatment: H. pylori infection
time: 6 h
passage: 8-12
chip-antibody: H2AXpS139 (Millipore, 05-636, lot: 2250524)
|
| Treatment protocol |
2 h prior to infection of AGS cells with the P12 strain of H. pylori, medium wsa replaced with RPMI-medium containing 0.1% FCS and infections were performed at an MOI of 50 for the indicated times. For irraditaion, the growth medium was replaced in a similar fashion, cells were irradiated for 11 min with a Cs-137 source (Gammacell 40 Exacotr; Nordion), corresponding to 10 Gy, followed by a 90 min recovery phase
|
| Growth protocol |
AGS cells were routinely grown in RPMI containing 10% FCS and replated every 2-3 days at a ratio of 1:3
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was corsslinked for 10 min in 1% Formaldehyd, before nuclei were isolated and protein-DNA-complexes were purified with the antibody
Libraries were constructed with NuGEN Ovation Ultralow Multiplex System (Part no 0330, 0331); after end-repair, adapter-ligation and quality control all samples were sequenced on an Illumina HiSeq2500
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
enirched regions were identified using HOMER (Heintz et al. 2010) with a window-size of 2500 bp and a minimal distance of 5000 bp
Genome_build: hg19
Supplementary_files_format_and_content: bed-files generated by HOMER's getPeaks tool using a window-size of 2.5kb and a minimal distance of 5kb
|
| |
|
| Submission date |
Mar 07, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas F Meyer |
| E-mail(s) |
tfm@mpiib-berlin.mpg.de
|
| Phone |
03028 460 404
|
| Organization name |
Max Planck Institute for Infection Biology
|
| Department |
Molecular Biology
|
| Street address |
Chariteplatz 1
|
| City |
Berlin |
| ZIP/Postal code |
10117 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE55699 |
Host genomic regions susceptible to damage during H. pylori infection |
|
| Relations |
| BioSample |
SAMN02677611 |
| SRA |
SRX482981 |
