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SRX19918984: GSM7158676: 12B_15934_minus4W_PBMC [re-analysis]; Macaca mulatta; RNA-Seq
12 ILLUMINA (Illumina HiSeq 3000) runs: 39.5M spots, 4G bases, 1.5Gb downloads

External Id: GSM7158676_r1
Submitted by: Genomics Core, Developmental and Cognitive Neuroscience, Yerkes National Primate Research Center
Study: Vpr attenuates antiviral immune responses and is critical for full pathogenicity of SIVmac239 in rhesus macaques
show Abstracthide Abstract
The accessory viral protein R (Vpr) is encoded by all primate lentiviruses. Vpr counteracts DNA repair pathways, modulates viral immune sensing, and induces cell-cycle arrest in cell culture. However, its impact in vivo is controversial. Here, we show that deletion of vpr is associated with delayed viral replication kinetics, rapid innate immune activation, development and maintenance of strong B cell responses, and generation of higher avidity p27 Gag antibodies in rhesus macaques. All wild-type SIVmac239 infected animals maintained high viral loads and five of six developed fatal immunodeficiency during ~80 weeks of follow-up. Lack of Vpr was associated with better preservation of CD4+ T cells, lower viral loads and an attenuated clinical course of infection in most animals. Our results demonstrate that Vpr contributes to efficient viral immune evasion and the full pathogenic potential of SIVmac in vivo. Inhibition of Vpr may improve humoral immune control of viral replication. Overall design: Six rhesus macaques were infected with a mutant SIVmac239 construct containing a large deletion of 101 nucleotides eliminating the vpr gene (?vpr), and six rhesus macaques were infected with wild type (wt) SIVmac239, and 10 rhesus macaques were uninfected. Blood samples (PBMC) were collected in two sets of experiments, A and B. Set A consists of wt (n=3) and ?vpr (n=3) infected animals at 2 and 24 weeks post-infection. For Set A, PBMC samples were also collected from uninfected control animals (n=10). Set B consists of blood samples from wt (n=3) and ?vpr (n=3) infected animals at both pre- (4 and 8 weeks) and post-infection (2 and 24 weeks) time-points.
Sample: 12B_15934_minus4W_PBMC [re-analysis]
SAMN34130414 • SRS17271775 • All experiments • All runs
Organism: Macaca mulatta
Library:
Name: GSM7158676
Instrument: Illumina HiSeq 3000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: RNA was extracted using Qiagen RNeasy Mini kits with DNase digest and QIAcube automation stations. RNA was quantified on NanoDrop 2000 spectrophotometer and the quality was assessed by Bioanalyzer analysis. Set A samples: Libraries were prepared using the Illumina TruSeq mRNA stranded kit, as per manufacturer's instructions, with 400 ng of total RNA as input. The amplified libraries were validated by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were normalized, pooled and sequenced on the Illumina HiSeq 3000 system employing a single-end 101 cycles run at average read depths of 16 million reads/sample. Set B samples: 10 ng of total RNA was used as input for cDNA amplification using 5' template-switch PCR with the Clontech SMART-Seq v4 Ultra Low Input RNA kit. Amplified cDNA was fragmented and appended with dual indexed bar codes using Illumina NexteraXT DNA Library Prep kits. The amplified libraries were validated by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were normalized, pooled and sequenced on the Illumina HiSeq 3000 system employing a single-end 101 cycles run at average read depths of 25 million reads/sample.
Runs: 12 runs, 39.5M spots, 4G bases, 1.5Gb
Run# of Spots# of BasesSizePublished
SRR241196642,932,425296.2M108.4Mb2023-12-06
SRR241196654,143,499418.5M162.6Mb2023-12-06
SRR241196664,115,595415.7M161.5Mb2023-12-06
SRR241196674,083,308412.4M160.7Mb2023-12-06
SRR241196682,973,086300.3M109.5Mb2023-12-06
SRR241196692,997,790302.8M110.4Mb2023-12-06
SRR241196702,881,256291M106.6Mb2023-12-06
SRR241196712,556,617258.2M97.7Mb2023-12-06
SRR241196722,894,306292.3M106.9Mb2023-12-06
SRR241196732,950,283298M108.3Mb2023-12-06
SRR241196742,866,399289.5M106.5Mb2023-12-06
SRR241196754,146,738418.8M162.9Mb2023-12-06

ID:
27293657

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