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Sample GSM3591800 Query DataSets for GSM3591800
Status Public on Jan 21, 2021
Title Naive CD4+ T cells 2 ATAC-Seq
Sample type SRA
 
Source name Peripheral blood
Organism Homo sapiens
Characteristics donor: 2
cell type: naive CD4+ T cells
activation status: Naive
Extracted molecule genomic DNA
Extraction protocol ATAC-seq was performed as described by Buenrostro et al (Nature Methods, 2013, PMID: 24097267).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing FASTQ files were output using standard Illumina protocols and software.
ATAC-seq reads were aligned to the human genome assembly (hg38) using Bowtie2 v2.2.5.
For samples with two technical replicates, the BAM were merged using the samtools merge function.
Mitochondrial reads, ummapped reads and low mappability (<30) reads were filtered out using the samtools view function.
Peaks were called using MACS2 –callpeak (with parameters -- nomodel, --extsize 200, and --shift 100) after merging all the filtered reads from all the samples and both donors into a single file.
The number of read counts overlapping each peak was then obtained for all ten samples using featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: Processed files are tab-delimited text (tsv) files. Columns represent the genomic location and the number of reads for each peak. Supplementary file PeakRegions.bed.gz provides the peak regions in BED format. Supplementary file PeakCounts.txt.gz provides read counts for all samples in a single file.
 
Submission date Feb 05, 2019
Last update date Jan 21, 2021
Contact name Gordon K Smyth
E-mail(s) smyth@wehi.edu.au
Phone (+61 3) 9345 2326
Fax (+61 3) 9347 0852
URL http://www.wehi.edu.au
Organization name Walter and Eliza Hall Institute of Medical Research
Department Bioinformatics
Lab Smyth
Street address 1G Royal Pde
City Parkville
State/province Vic
ZIP/Postal code 3052
Country Australia
 
Platform ID GPL18573
Series (2)
GSE126113 ATAC-seq profiles of B cells and naive and activated T cells from human peripheral blood
GSE126117 RNA-seq, ATAC-seq and Hi-C profiles of B cells and naïve and activated T cells from human peripheral blood
Relations
BioSample SAMN10875774
SRA SRX5336496

Supplementary file Size Download File type/resource
GSM3591800_CD4T_naive2.txt.gz 1.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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