|
| Status |
Public on Sep 30, 2017 |
| Title |
CHL1_BRD4_D4_01 |
| Sample type |
SRA |
| |
|
| Source name |
melanoma cancer cell line CHL-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: CHL-1
tumor type: melanoma
tissue: skin
chip antibody: anti-BRD4 (Bethyl Labs, A301-985A100)
|
| Treatment protocol |
CHL-1 cells were treated for 4 hr with 500 nM BAY 1238097, OTX-015, or DMSO
|
| Growth protocol |
CHL-1 melanoma cells were obtained from the American Type Culture Collection (ATCC) and were routinely grown DMEM medium in the presence of 10% (v/v) fetal calf serum (Life Technologies) at 37 °C and in 5% CO2 atmosphere.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
One 15 cm cell culture dish with 80% confluent cells was used per IP. ChIP DNA preparation for sequencing was carried out as described previously in Nagarajan et al. (Cell Rep. 2014 Jul 24;8(2):460-9) with the following changes: cross-linked chromatin was sheared to 200-800 base pair fragments using sonication (30 sec on/30 sec off, high power, 2 x 7.5 minutes with a water bath change between the two cycles) in a Biorupter sonicator UCD-200. 1.5 µg antibodies (anti-BRD4 [Bethyl Labs, A301-985A100]; anti-H3K27ac [Diagenode, C15410174]) were used per IP. DNA was purified using a PCR purification kit (Qiagen)
TrueSeq® ChIP Sample Preparation Guide (Illumina).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
D4=BAY123897
|
| Data processing |
paired-end genome wide sequencing data were aligned to the human reference genome (assembly hg19) using Bowtie2 software and sorted and indexed using SAMtools
Peak calling was done using the Model-bases analysis for ChIP-seq (MACS2) software. Broad peaks from H3K27Ac were called using MACS2 broad mode. MACS2 was used to generate enrichment pileups (log likelihood ratio (logLR)) of treatment vs. input control samples. A pseudocount of 0.00001 was added to avoid log10(0) during logLR calculation.
ChIP-seq tracks were generated using the Integrative Genomics Viewer software (Thorvaldsdottir et al. 2013). Heatmaps and line plots were generated using the seqplots software (http://przemol.github.io/seqplots).
Genome_build: hg19
Supplementary_files_format_and_content: bw (see UCSC file format FAQ http://www.genome.ucsc.edu/FAQ/FAQformat.html) files reporting enrichment pileup as log likelihood ratio
|
| |
|
| Submission date |
Mar 01, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ralf Lesche |
| E-mail(s) |
ralf.lesche@bayer.com
|
| Organization name |
Bayer Pharma AG
|
| Street address |
Muellerstr 178
|
| City |
Berlin |
| ZIP/Postal code |
13342 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE95585 |
ChIPSeq data from melanoma cancer cell line CHL-1 after Bromodomain and extra terminal (Bet) domain inhibitor treatment |
|
| Relations |
| BioSample |
SAMN06470148 |
| SRA |
SRX2606560 |
