|
| Status |
Public on May 12, 2016 |
| Title |
ChIP-seq for transcription factor E2A |
| Sample type |
SRA |
| |
|
| Source name |
Human Ramos cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Ramos
chip antibody: anti-E2A (sc-349; Santa Cruz Technologies)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
20 million cells from the human Ramos cell line were crosslinked by the addition of 1% formaldehyde at room temperature for 10 min and quenched with 0.25M glycine followed by sonication and immunoprecipitation with 10 μg of anti-E2A (sc-349; Santa Cruz Technologies).
DNA fragments were blunt-end ligated to the Illumina adaptors, amplified, and sequenced with an Illumina HiSeq Sequencer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
E2A_ChIPseq
|
| Data processing |
Sequence reads were mapped to human genome hg19 using the Subread aligner. Only uniquely mapped reads were retained.
E2A binding peaks were identified using MACS2 v2.1.0 program with a p-value cutoff of 1e-5. Genes with binding peaks falling within between 20 kilobases upstream and 5 kilobases downstream of the gene body were considered to be E2A binding targets. NCBI RefSeq human annotation build 37.2 was used to obtain chromosomal coordinates of genes. Binding peaks were assigned to genes using the featureCounts program. Gene symbols were used to match genes in ChIP-seq data with those in RNA-seq data.
Genome_build: hg19
Supplementary_files_format_and_content: A BED file including E2A binding regions
Supplementary_files_format_and_content: A .txt file including E2A binding regions (MACS-generated)
|
| |
|
| Submission date |
Sep 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei Shi |
| E-mail(s) |
Wei.Shi@onjcri.org.au
|
| Organization name |
Olivia Newton John Cancer Research Institute
|
| Department |
Bioinformatics and Cancer Genomics
|
| Street address |
Level 5, ONJ Cancer Centre, 145 Studley Rd
|
| City |
Heidelberg |
| State/province |
VIC |
| ZIP/Postal code |
3084 |
| Country |
Australia |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE72828 |
Dynamic changes in E protein activity orchestrate germinal center and plasma cell development [ChIP-Seq] |
| GSE72832 |
Dynamic changes in E protein activity orchestrate germinal center and plasma cell development |
|
| Relations |
| BioSample |
SAMN04043984 |
| SRA |
SRX1212540 |
