|
| Status |
Public on Apr 01, 2014 |
| Title |
γ-H2AX_IL2aCD3aCD28_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
CD4+ T cells activated by IL-2+aCD3+aCD28
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD4+ T cells
chip antibody: gamma H2A.X (Abcam, ab2893, lot GR43146-1)
|
| Treatment protocol |
CD4+ T cells were incubated with IL-2, either alone or alongside anti-CD3 and anti-CD28 antibodies.
|
| Growth protocol |
CD4+ T cells were isolated from human PBMC and maintain in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS). Hela-S3 cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and purmomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
DNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2.
Sequence reads were obtained and mapped to the hg19 human genome using the Illumina Genome Analyzer Pipeline.
All reads uniquely mapped to the gnome with two or fewer mismatches were retained and extended to the library fragment size (200 bp) to create the BED files.
Genome_build: hg19
Supplementary_files_format_and_content: BED files
|
| |
|
| Submission date |
Feb 13, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jungmin Seo |
| Organization name |
Omicsis.Inc
|
| Department |
Bioinformatics Research Institute
|
| Street address |
#211, BVC, KRIBB, Eoung-dong, Yuseong-gu
|
| City |
Daejeon |
| ZIP/Postal code |
305-806 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE44309 |
Whole-genome landscape of histone H2AX and γ-H2AX along with related factors in activated cells |
|
| Relations |
| SRA |
SRX237288 |
| BioSample |
SAMN01920647 |
