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SRX24348319: GSM8224596: 1_A11263_SIV_CD4N ATAC; Macaca nemestrina; ATAC-seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 15.7M spots, 4.7G bases, 1.5Gb downloads

External Id: GSM8224596_r1
Submitted by: NIAID Collaborative Bioinformatics Resource (NCBR), Integrated Data Sciences Section (IDSS), NIAID
Study: SIV infection and ARV treatment reshape the transcriptional and epigenetic profile of naïve and memory T cells in vivo (ATAC-Seq)
show Abstracthide Abstract
Here we use RNAseq and ATACseq to study the transcriptomics and epigenetic landscape of longitudinally sampled naïve and memory CD4+ and CD8+ T cells in two species of non-human primates prior to SIV infection, during chronic SIV infection, and after administration of ARVs. We find that SIV infection leads to significant alteration to the transcriptomic profile of all T cell subsets that are only partially reversed by administration of ARVs. Epigenetic changes were more apparent in animals with longer periods of untreated SIV infection and correlated well with changes in corresponding gene expression. Known SIV integration sites did not vary due to SIV status but did contain more open chromatin in rhesus macaque memory T cells, and the expression of proteasome-related genes at the pre-SIV timepoint correlated with subsequent viremia. Overall design: RNAseq and ATACseq of longitudinally sampled naïve and memory CD4+ and CD8+ T cells in rhesus macaques and pig-tail macaques prior to SIV infection, during chronic SIV infection, and after administration of ARVs.
Sample: 1_A11263_SIV_CD4N ATAC
SAMN41062686 • SRS21107301 • All experiments • All runs
Library:
Name: GSM8224596
Instrument: Illumina NovaSeq 6000
Strategy: ATAC-seq
Source: GENOMIC
Selection: other
Layout: PAIRED
Construction 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).
Runs: 1 run, 15.7M spots, 4.7G bases, 1.5Gb
Run# of Spots# of BasesSizePublished
SRR2878388915,672,3074.7G1.5Gb2024-05-10

ID:
32662975

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