|
| Status |
Public on Feb 02, 2020 |
| Title |
IRF4_ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
TL-OM1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: TL-OM1 cells
cell type: adult T-cell leukemia/lymphoma cell line
chip antibody: IRF-4 Antibody (M-17): sc-6059
|
| Treatment protocol |
TL-Om1 cells were cross-linked with formaldehyde for 10 min. Lysates were clarified from sonicated nuclei and IRF4-DNA complexes were isolated with antibody. A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment.
|
| Growth protocol |
TL-Om1 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction from the IRF4 ChIP-seq samples and sequencing of paired-end 49-bp-long reads by the Illumina HiSeq 4000 were performed at BGI Biotech Solutions Co. Ltd (Hong Kong, China).
Single-end ChIP-Seq sequencing
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
ChIP-seq reads were mapped to human hg19 reference genome using bowtie2 program with default parameters.
Aligned ChIP-seq reads were remove duplicate with samtools rmdup package.
ChIP-Seq peaks were called with MACS2 software, version 2.1.1.2016030. Threshold for the peaks called is P-value < 1E-9
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files of IRF4 called with MACS2 1E-9
|
| |
|
| Submission date |
Jul 08, 2018 |
| Last update date |
Feb 03, 2020 |
| Contact name |
Tze King Tan |
| Organization name |
National University of Singapore
|
| Department |
Cancer Science Institute
|
| Lab |
Takaomi Sanda Lab
|
| Street address |
14 Medical Drive
|
| City |
Singapore |
| ZIP/Postal code |
117599 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL23227 |
| Series (2) |
| GSE116763 |
IRF4 ChIP-seq analysis in TL-Om1 cells |
| GSE133042 |
Oncogenic Regulatory Network Driven by IRF4 and NF-kappaB in Adult T-cell Leukemia/Lymphoma |
|
| Relations |
| BioSample |
SAMN09629829 |
| SRA |
SRX4365999 |
