NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7278700 Query DataSets for GSM7278700
Status Public on Aug 07, 2023
Title Wildtype 2
Sample type SRA
 
Source name CD8
Organism Mus musculus
Characteristics cell line: CD8
cell type: memory type
genotype: wildtype
chip antibody: Acetyl histone antibodies
Extracted molecule genomic DNA
Extraction protocol ABCAM (AB1191)
Chip-Seq libraries were constructed from 50 ng of ChIP DNA using Ovation Ultralow System V2 1-96 with 15 cycles of PCR amplification. The final libraries were twice purified using Ampure XP PCR Purification Beads (Agencourt). The libraries were pooled and then quantitated by qPCR. The pool balance was checked by performing a MiSeq run using a MiSeq Nano kit, version 2. The percentage of each library in the pool was determined from the demultiplexing and was used to rebalance the pool before sequencing. The pooled libraries were sequenced on a NovaSeq 6000 using version 1.5 chemistry to achieve a minimum of 37 million 51-base reads. The data was processed using RTA version 3.4.4.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Description acetyl K18
Data processing Quality control checks were performed using FastQC (0.11.9) on raw sequence data in fastq files generated from sequencer
The fastq files were aligned to the mouse reference genome (GRCm38 or mm10) using BWA-mem(0.7.17)
The output BAM files were filtered to retain only uniquely mapping reads using Samtools(1.15.1) view
The reads overlapping with backlisted regions were removed from bam files using Samtools view. Blacklisted regions were downloaded from the ENCODE project. (https://www.encodeproject.org/files/ENCFF547MET/)
broad peak calling was performed using MACS2(2.2.6)
Diffbind(3.2) was used to identify the differentially enriched peaks between Wildtype and PDH_Mutant samples
The peak profiles were annotated using ChIPseeker(1.28.3) in R (version 4.1.0)
For visualization of peaks in UCSC Genome Browser, the bam files were first sorted and indexed using Samtools sort and Samtools index respectively and the bedGraph files were converted to bigWig files using UCSC bedGraphToBigWig tool
Assembly: GRCm38
Supplementary files format and content: broadPeak,bigWig
 
Submission date May 01, 2023
Last update date Aug 07, 2023
Contact name Peter McGuire
E-mail(s) peter.mcguire@nih.gov, payal.banerjee@nih.gov
Organization name NHGRI
Street address 10 Center Dr
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL24247
Series (2)
GSE231433 Pyruvate dehydrogenase complex integrates the metabolome and epigenome in memory CD8+ T cell differentiation in vitro [ChIP-Seq]
GSE231556 Pyruvate dehydrogenase complex integrates the metabolome and epigenome in memory CD8+ T cell differentiation in vitro
Relations
BioSample SAMN34505864
SRA SRX20176961

Supplementary file Size Download File type/resource
GSM7278700_macs2_sorted_broad_sortedS9_filtered_peaks.broadPeak.gz 222.2 Kb (ftp)(http) BROADPEAK
GSM7278700_sortedS9_filtered.bw 445.1 Mb (ftp)(http) BW
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