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Sample GSM3144749 Query DataSets for GSM3144749
Status Public on Feb 18, 2019
Title ChIP_H3K27ac_HS895T
Sample type SRA
 
Source name Melanoma cell line
Organism Homo sapiens
Characteristics cell line: HS895T
time point: Base line
Growth protocol Cells were kept at 37°C, with 5% CO2 and were maintained in Ham's F10 nutrient mix (Thermo Fished Scientific) supplemented with 10% fetal bovine serum (FBS; Invitrogen) and 100 µg ml-1 penicillin/streptomycin (Thermo Fished Scientific).
Extracted molecule genomic DNA
Extraction protocol Chromatin was extracted using the MagnaChIP-seq kit (millipore). 4 µg of antibody was used on 2 million cells. Sonication was performed for 12 cycles, 30 sec pulses using the biorupter.
Illumina TruSeq
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description ChIP_H3K27ac_HS895T.nofirst5bp.minMQ4.sorted.bw
Data processing Reads obtained from H3K27Ac ChIP-seq were mapped to the genome using Bowtie2 (v2.1.0). The sensitive-local setting for Bowtie2 was used to correct for a high percentage of mismatches at the start of a read. bigWig files were generated from bam files using BEDTools (v2.17.0) and the scores represent the coverage. We used as control the merged control profiles of five cell lines, namely A375, MM011, MM032, MM047 and MM057. We used MACS2 (v2.0.10) with the command 'callpeak -t ChIPseq_file -c Control_file -g hs --qvalue 0.001 -n name'.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated from bam files using BEDTools (v2.23.0) and the scores represent the coverage. Bedfiles supplied with FDR0.001
 
Submission date May 16, 2018
Last update date Feb 18, 2019
Contact name Stein Aerts
E-mail(s) stein.aerts@kuleuven.vib.be
Organization name KU Leuven
Street address O&N4 Herestraat 49 PO Box 602
City Leuven
ZIP/Postal code 3000
Country Belgium
 
Platform ID GPL16791
Series (1)
GSE114557 cisTopic: cis-regulatory topic modelling on single-cell ATAC-seq data
Relations
BioSample SAMN09216359
SRA SRX4091684

Supplementary file Size Download File type/resource
GSM3144749_ChIP_H3K27ac_HS895T.nofirst5bp.minMQ4.sorted.bw 69.8 Mb (ftp)(http) BW
GSM3144749_ChIP_H3K27ac_HS895T_peaks.narrowPeak.gz 45.3 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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