|
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
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|
|
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 |