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Series GSE264656 Query DataSets for GSE264656
Status Public on May 10, 2024
Title SIV infection and ARV treatment reshape the transcriptional and epigenetic profile of naïve and memory T cells in vivo (ATAC-Seq)
Organisms Macaca mulatta; Macaca nemestrina
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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.
 
Contributor(s) Rahmberg AR, Markowitz TE, Mudd JC, Ortiz AM, Brenchley JM
Citation(s) 38780248
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
 
Platforms (2)
GPL27943 Illumina NovaSeq 6000 (Macaca mulatta)
GPL33261 Illumina NovaSeq 6000 (Macaca nemestrina)
Samples (120)
GSM8224596 1_A11263_SIV_CD4N ATAC
GSM8224597 2_A11263_SIV_CD4M ATAC
GSM8224598 3_A11263_SIV_CD8N ATAC
Relations
BioProject PRJNA1103756

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Supplementary file Size Download File type/resource
GSE264656_RAW.tar 52.5 Gb (http)(custom) TAR (of BW, NARROWPEAK)
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Raw data are available in SRA

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