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Sample GSM7655042 Query DataSets for GSM7655042
Status Public on Jul 25, 2023
Title Day3 effector, 1 (ATAC-seq)
Sample type SRA
 
Source name spleen
Organism Mus musculus
Characteristics tissue: spleen
cell type: CD8+ T cell
Extracted molecule genomic DNA
Extraction protocol Sorted cells were centrifuged and frozen in ATAC freezing buffer and stored at -80°C. For processing, cells were thawed, centrifuged, washed with PBS and lysed. Nuclei were then subjected to tagementation and purification.
Purfied tagmented DNA was PCR amplifed using Illumina indexed primers and NEBNext High-Fidelity 2X PCR Master Mix. Pooled libraries were sequenced on a NextSeq 500 High150 cycle kit with paired end sequencing (read 1: 74 cycles, read 2: 74 cycles, index 1: 10 cycles, index 2: 10 cycles)
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Raw fastq files were processed and aligned to the mm10 mouse genome using the PEPATAC (v0.10.3) pipeline, which uses bowtie2 for alignment. Unmapped, unpaired, and mitochondrial reads were removed.
Following alignment, peak calling, merging across all samples, and annotation was performed using HOMER (v4.10). The peaks.txt processed data files represent the individual sample peak counts prior to identifying consensus peaks. The HOMER commands used to generate peak counts from bam files were: makeTagDirectory, findPeaks (parameters: -style factor -o auto), mergePeaks (parameters: -d 150), annotatePeaks.pl (parameters: mm10 -size "given" -raw -d)
Differentially accessible regions were identified using DESeq2.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: The peaks.txt file for each sample was generated from HOMER findPeaks and contains columns with peakID, peak information, and normalized counts.
 
Submission date Jul 20, 2023
Last update date Jul 25, 2023
Contact name Kathleen Abadie
E-mail(s) abadiek@uw.edu
Organization name University of Washington
Department Bioengineering
Lab Kueh Lab
Street address 3720 15th Ave NE
City Seattle
State/province Washington
ZIP/Postal code 98195
Country USA
 
Platform ID GPL19057
Series (2)
GSE237827 Flexible and scalable control of T cell memory by a reversible epigenetic switch (ATAC-seq)
GSE237830 Flexible and scalable control of T cell memory by a reversible epigenetic switch
Relations
BioSample SAMN36656117
SRA SRX21106725

Supplementary file Size Download File type/resource
GSM7655042_C3_D3_S3_smooth.bw 2.5 Gb (ftp)(http) BW
GSM7655042_S3_peaks.txt.gz 1.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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