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Sample GSM4260071 Query DataSets for GSM4260071
Status Public on Oct 20, 2020
Title Control_H3K27Ac_ChIP_B
Sample type SRA
 
Source name Oligodendrocyte progenitor cells (OPCs)
Organism Mus musculus
Characteristics cell type: epiblast stem cell derived OPCs
antibody: H3K27Ac (abcam4729, 9ug per ChIP
number of cells per chip: 5-20 million OPCs
Treatment protocol Comparison between control and Vhl knockout OPCs.
Growth protocol OPCs were grown in DMEM F12 supplemented with N2max and B27 and Fgf2 and Pdgfa.
Extracted molecule genomic DNA
Extraction protocol Nuclei isolation and chromatin shearing were performed using the Covaris TruChIP protocol following manufacturer’s instructions for the “high-cell” format. In brief, 5-20 million cells were crosslinked in “Fixing buffer A” supplemented with 1% fresh formaldehyde for 10 minutes at room temperature with oscillation and quenched for 5 minutes with “Quench buffer E.” These cells were then washed with PBS and either snap frozen and stored at -80, or immediately continued to nuclei extraction and shearing per the manufacturer protocol. The samples were sonicated with the Covaris S2 using the following settings: 5% Duty factor 4 intensity for four 60-second cycles. Sheared chromatin was cleared and incubated overnight at 4 degrees with antibody that was pre-incubated with protein G magnetic DynaBeads (ThermoFisher). Protein G dynabeads were then washed, eluted, reverse cross-linked and treated with RNase A followed by proteinase K. ChIP DNA was purified using Ampure XP beads (Aline Biosciences, C-1003-5) and then used to prepare illumina sequencing libraries.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
 
Description CRISPR-Control-OPCs
Data processing Reads were quality and adapter trimmed using Trim Galore! Version 0.4.1.
Trimmed reads were alighed to mm10 with Bowtie2 version 2.3.2.
Duplicate reads (potential artifacts of PCR in library preparation) were removed using Picard MarkDuplicates.
Genome_build: mm10
Supplementary_files_format_and_content: bigWIG files were generated using Deeptools bamCoverage with reads per genome coverage normalization. BED files in a broadPeaks format from MACS2.
 
Submission date Jan 10, 2020
Last update date Oct 20, 2020
Contact name Paul Tesar
E-mail(s) paul.tesar@case.edu
Organization name Case Western Reserve University
Department Genetics & Genome Sciences
Street address 10900 Euclid Ave.
City Cleveland
State/province Ohio
ZIP/Postal code 44106
Country USA
 
Platform ID GPL21103
Series (2)
GSE143472 Non-Canonical Targets of HIF1a Impair Oligodendrocyte Progenitor Cell Function [ChIP-Seq]
GSE143474 Non-Canonical Targets of HIF1a Impair Oligodendrocyte Progenitor Cell Function
Relations
BioSample SAMN13826214
SRA SRX7541939

Supplementary file Size Download File type/resource
GSM4260071_Control_H3K27Ac_B_BW.bw 377.9 Mb (ftp)(http) BW
GSM4260071_Control_H3K27Ac_B_Peak.broadpeak.gz 659.7 Kb (ftp)(http) BROADPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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