|
| Status |
Public on Dec 31, 2017 |
| Title |
SGE_ATAC_130 |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood mononuclear cells
|
| Organism |
Macaca mulatta |
| Characteristics |
cell type: peripheral blood mononuclear cells
subject_id: RFm12
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 |
| E-mail(s) |
[email protected]
|
| 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] |
|
| Relations |
| BioSample |
SAMN05240277 |
| SRA |
SRX1840958 |
