GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM3163871 Query DataSets for GSM3163871
Status Public on Oct 23, 2019
Title ATACseq_3TP_0hr_rep2
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 Cell nuclei were isolated as described previously (Buenrostro et al., 2013). 50,000 cell nuclei were used for library construction.
Chromatin was tagmented using Illumina Nextera kit as described previously (Buenrostro et al., 2013).
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
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 bowtie2 version 2.2.9 (Langmead and Salzberg, 2012), 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)).
After alignment of the reads to the reference genome, reads aligned to the positive strand were moved +4 bp, and reads aligning the negative strand were moved -5bp.
For each of our two replicate pairs per time point, we called peaks using MACS2 version 2.1.0 (Zhang et al., 2008) with default parameters (setting the FDR to 0.05 and default hg19 human genome size).
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak
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 GPL16791
Series (2)
GSE115044 Massively parallel characterization of regulatory dynamics during neural induction [ATAC-seq]
GSE115046 Massively parallel characterization of regulatory dynamics during neural induction
BioSample SAMN09276510
SRA SRX4136833

Supplementary file Size Download File type/resource
GSM3163871_ATACseq_3TP_0hr_rep2_peaks.narrowPeak.gz 916.2 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap