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Sample GSM2199356 Query DataSets for GSM2199356
Status Public on Dec 31, 2017
Title SGE_ATAC_124
Sample type SRA
Source name peripheral blood mononuclear cells
Organism Macaca mulatta
Characteristics cell type: peripheral blood mononuclear cells
subject_id: RJs11
study phase: phase 2
Treatment protocol PBMCs were seeded at 500,000 cells per mL of media and incubated at 35C for 90 minutes.
Growth protocol we drew 4 mL of blood from each female and purified the PBMC fraction using density gradient centrifugation.
Extracted molecule genomic DNA
Extraction protocol ATAC-seq libraries were prepared from 50,000 cells per sample as described in Buenrostro et al 2013, but skipping the cell lysis step, which has been shown to reduce the proportion of mitochondrial reads in the final library.
Libraries were barcoded, multiplexed, and sequenced on an Illumina NextSeq using paired-end, 38 bp reads.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
Data processing Library strategy: ATAC-Seq
Reads were mapped to MacaM using the bwa-mem algorithm with default settings
Open chromatin regions were identified using MACS2 (--nomodel --keep-dup all -q 0.05 -f BAMPE) after merging data from all three samples into a single alignment file and removing all reads that mapped to the mitochondria. We called peaks at a 5% FDR threshold
Genome_build: MacaM
Supplementary_files_format_and_content: [.bed] peaks
Submission date Jun 13, 2016
Last update date May 15, 2019
Contact name Noah Snyder-Mackler
Phone 3025938430
Organization name Arizona State University
Lab Snyder-Mackler
Street address 427 East Tyler Mall
City Tempe
State/province AZ
ZIP/Postal code 85281
Country USA
Platform ID GPL21120
Series (1)
GSE83306 Social status alters immune regulation and response to infection [PBMC_ATACseq]
BioSample SAMN05240276
SRA SRX1840957

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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