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| Status |
Public on Oct 23, 2019 |
| Title |
ATACseq_7TP_72hr_rep1 |
| Sample type |
SRA |
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| Source name |
Neural progenitor cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: H1 hESC-derived neural progenitor cells
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| Treatment protocol |
Neural induction was performed according to dual-Smad inhibition protocol (Chambers et al., 2009) for up to 72 hours.
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| Growth protocol |
H1 hESCs were culture in mTeSR1 media on matrigel coated dishes.
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| 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).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| 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
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| Submission date |
May 29, 2018 |
| Last update date |
Oct 23, 2019 |
| Contact name |
Anat Kreimer |
| E-mail(s) |
anat.kreimer@berkeley.edu
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| Organization name |
University of California, Berkeley
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| Street address |
378 Stanley Hall
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| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE115044 |
Massively parallel characterization of regulatory dynamics during neural induction [ATAC-seq] |
| GSE115046 |
Massively parallel characterization of regulatory dynamics during neural induction |
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| Relations |
| BioSample |
SAMN09276514 |
| SRA |
SRX4136842 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3163880_ATACseq_7TP_72hr_rep1_peaks.narrowPeak.gz |
1.1 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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