|
| Status |
Public on Jul 18, 2018 |
| Title |
16 hr TNF-a BRD4 ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
SW480 Cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SW480
cell type: Human Colon Cancer Cell Line
treated with: 12.5 ng ml-1 TNF-α for 16 hr
chip antibody: Anti-BRD4: Bethyl laboratories; cat# A301-985A100; lot# A301-985A100-6
|
| Treatment protocol |
cells were treated with 12.5 ng ml-1 TNF-α(Shenandoah Biotechnology) for 0 or 16 hr before harvesting for ChIP-seq analyses.
|
| Growth protocol |
Human SW480 cells were grown in Dulbecco’s modified Eagle medium (DMEM, Gibco) medium supplemented with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates from sonicated nuclei were prepared and protein-DNA complexes were IP'd overnight with BRD4 antibody.
ChIP-seq libraries were prepared according to Illumina's ChIP Truseq protocol. Briefly, ChIP DNA was end-repaired and adaptors were ligated to the ends of the DNA fragments. Adaptor-ligated ChIP DNA fragments with average size of 350 bp were used to construct libraries and single-end sequenced on Illumina HiSeq 4000.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Sequenced reads were mapped to the hg38 human reference genome using Bowtie2 software and default parameters.
Mapped reads were then processed to make tag directories using the HOMER module. PCR duplications were removed and only uniquely mapped reads were kept for further analyses.
Genome browser files for resulting reads were generated by using the makeUCSCfile module from HOMER.
Enrichment for BRD4 and histone modification deposition were called using findPeaks module from HOMER using preset parameters for transcription factors and histones, respectively and compared to the input samples.
Deeptools were used to generate heatmaps.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Feb 12, 2018 |
| Last update date |
Jul 18, 2018 |
| Contact name |
Shannon M Lauberth |
| E-mail(s) |
[email protected]
|
| Organization name |
UCSD
|
| Department |
Biological Sciences
|
| Lab |
Lauberth Lab
|
| Street address |
9500 Gilman Drive #0322, Bonner Hall 3202
|
| City |
San Diego |
| State/province |
California |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE110473 |
RNAs Interact with BRD4 to Promote Enhanced Chromatin Engagement and Transcription Activation |
|
| Relations |
| BioSample |
SAMN08518278 |
| SRA |
SRX3680731 |
