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Sample GSM3163860 Query DataSets for GSM3163860
Status Public on Oct 23, 2019
Title H3K27me3_ChIPSeq_rep2_72hr
Sample type SRA
Source name Neural progenitor cells
Organism Homo sapiens
Characteristics cell type: H1 hESC-derived neural progenitor cells
Treatment protocol Neural induction was performed according to dual-Smad inhibition protocol (Chambers et al., 2009) for up to 72 hours.
Growth protocol H1 hESCs were culture in mTeSR1 media on matrigel coated dishes.
Extracted molecule genomic DNA
Extraction protocol Cells were crosslinked with 1% formaldehyde. Chromatin was shared with Covaris S2 sonicator. ChIP was performed using LowCell# ChIP kit (Diagenode). H3K27ac (Abcam, ab4729) and H3K27me3 antibodies (EMD Millipore, 07-449) were used.
Library construction was performed using ThruPLEX DNA-seq kit (Rubicon Genomics) accoring to manufacture's protocol.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
Data processing We used the FASTQC pipeline (Version 0.3.2; Babraham Bioinformatics) on our reads, and aligned them to the reference genome (hg19) with bowtie version 1.1.1 (Langmead et al., 2009) , retaining only reads that mapped to a unique position in the genome [“–m 1”].
We marked duplicate reads in the bam files using PICARD and checked for contamination of primer sequences using Trimmomatic (Version 0.3.2; (Bolger et al., 2014)).
For each of our H3K27ac and H3K27me3 ChIP-seq replicate pairs per time points peaks were called using MACS2 version 2.1.0 (Zhang et al., 2008), with the relevant control input file with default parameters (setting the FDR to 0.05 and default hg19 human genome size).
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak or broadPeak
Submission date May 29, 2018
Last update date Oct 23, 2019
Contact name Anat Kreimer
Organization name University of California, Berkeley
Street address 378 Stanley Hall
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
Platform ID GPL20301
Series (2)
GSE115043 Massively parallel characterization of regulatory dynamics during neural induction [ChIP-seq]
GSE115046 Massively parallel characterization of regulatory dynamics during neural induction
BioSample SAMN09276527
SRA SRX4136884

Supplementary file Size Download File type/resource
GSM3163860_rep2_72hr_K27me3_peaks.broadPeak.gz 276.0 Kb (ftp)(http) BROADPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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