|
| Status |
Public on Oct 23, 2019 |
| Title |
input_DNA_rep1_72hr_Input |
| 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 |
| E-mail(s) |
anat.kreimer@berkeley.edu
|
| 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 |
|
| Relations |
| BioSample |
SAMN09276544 |
| SRA |
SRX4136870 |
