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Sample GSM2516778 Query DataSets for GSM2516778
Status Public on Sep 30, 2017
Title CHL1_input_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: 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).
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 (
Genome_build: hg19
Supplementary_files_format_and_content: bw (see UCSC file format FAQ files reporting enrichment pileup as log likelihood ratio
Submission date Mar 01, 2017
Last update date May 15, 2019
Contact name Ralf Lesche
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
BioSample SAMN06470144
SRA SRX2606562

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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