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Sample GSM8224695 Query DataSets for GSM8224695
Status Public on May 10, 2024
Title 100_Rh4345_ARV_CD8M ATAC
Sample type SRA
 
Source name peripheral blood
Organism Macaca mulatta
Characteristics tissue: peripheral blood
cell type: CD8 memory T cell
disease state: ARV
Extracted molecule genomic DNA
Extraction protocol Up to 10,000 sorted cells from each population were pelleted and resuspended in 2x Tagmentation Buffer (Illumina), 0.02% Digitonin, and 0.1% Tween-20, with Tagment DNA TDE1 Enzyme (Illumina) and incubating at 37°C for one hour. The mix was then incubated with proteinase K for 30 minutes at 40°C.
High molecular weight DNA was removed with a 0.7x selection ratio of Agencourt AMPureXP beads (Beckman Coulter) and low molecular weight DNA was isolated from the remainder with a 1.2x selection ratio. Library amplification was performed with KAPA HiFi HotStart ReadyMix (KAPA) and i5 and i7 indexing primers (Nextera DNA CD Indexes) for 11-15 total cycles depending on the sample concentration reached after 5 cycles (KAPA Library Quantification kit). Library DNA was purified with a 1x selection ratio of AMPureXP beads. The final library was verified by High Sensitivity DNA Bioanalyzer (Agilent).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description 100_Rh4345_ARV_CD8M
Data processing ATAC-seq samples were sequenced as 151bp paired-end libraries on a Novaseq S4. All samples had over ?? million reads.
Samples were trimmed for adapters using Cutadapt v 1.18 before alignment. The trimmed reads were aligned to the RheMac10 reference using Bowtie2 v2.3.4.1 with flag -k 10.
Assembly: RheMac10
Supplementary files format and content: The peaks were called using Genrich v0.6 with the following flags -j -y -r -v -d 150 -m 5 -e chrM,chrY.
Supplementary files format and content: Genrich-produced bedgraphs were normalized by library size (reads per million sequenced reads, RPM) for visualization.
 
Submission date Apr 23, 2024
Last update date Jul 01, 2024
Contact name Jason Brenchley
E-mail(s) jbrenchl@niaid.nih.gov
Organization name NIAID
Street address 4 Center Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL27943
Series (1)
GSE264656 SIV infection and ARV treatment reshape the transcriptional and epigenetic profile of naïve and memory T cells in vivo (ATAC-Seq)
Relations
BioSample SAMN41062587
SRA SRX24348402

Supplementary file Size Download File type/resource
GSM8224695_100_Rh4348_ARV_CD8M.genrich.RPM.bw 573.3 Mb (ftp)(http) BW
GSM8224695_100_Rh4348_ARV_CD8M.narrowPeak.gz 918.1 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA

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