|
Status |
Public on Sep 30, 2017 |
Title |
CHL1_input_D4_02 |
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: none
|
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).
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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
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|
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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 |
SAMN06470129 |
SRA |
SRX2606571 |