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| Status |
Public on Feb 09, 2022 |
| Title |
RSr15_d-10 |
| Sample type |
SRA |
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| Source name |
Rhesus macaque RSr15
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| Organism |
Macaca mulatta |
| Characteristics |
cell type: PBMC
disease state: SIV-
treatment: none
time: 10 days pre-infection
animal: Indian-origin, specific-pathogen-free rhesus macaques
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| Treatment protocol |
A neutralizing anti-IL-10 monoclonal antibody (mAb) was administered in vivo to SIV-infected, ART-treated RMs. Six RMs were i.v. infected with SIVmac239 and at d35 post-infection began a daily ART regimen. At d211 post-infection, all RMs were i.v. administered 10 mg/kg of a rhesus-recombinant anti-IL-10 mAb. Four weeks later (d238 post-infection), all RMs received a second infusion of the anti-IL-10 mAb, which was dose-escalated to 20 mg/kg.
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| Growth protocol |
PBMCs at pre-infection (d-20 p.i.) were stored in RLT buffer (QIAGEN) at -80°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using QIAGEN RNeasy kits. Polyadenylated transcripts were purified on oligo-dT magnetic beads, fragmented, reverse transcribed using random hexamers, and incorporated into barcoded cDNA libraries based on the Illumina TruSeq platform.
Libraries were validated by microelectrophoresis and quantified, pooled, and clustered on Illumina TruSeq v3 flow cells. Clustered flow cells were sequenced on an Illumina HiSeq 1000 in 100-base single-read reactions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
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| Data processing |
RNA-Seq data was collected at the Yerkes Nonhuman Primate Genomics Core laboratory.
Alignment was performed using STAR version 2.3.0e; parameters were set using the annotation as a splice junction reference, and unannotated, noncanonical splice junction mappings and nonunique mappings were removed from downstream analysis. Transcripts were annotated using MacaM assembly and annotation, version 7.6. Transcript assembly, abundance estimates, and differential expression analysis were performed using Cufflinks, version 2.1.1, and Cuffdiff. RNA-seq data are expressed as fragments per kilobase mapped (FPKM), which is the default output by Cufflinks/Cuffdiff, in which reads and fragments mapping to an individual gene are normalized by the total number of kilobases that map to the reference genome for an individual sample; this calculation minimizes bias due to differences in sequencing depth between samples.
Genome_build: New Rhesus Genome (MacaM version 7.6) (https://www.unmc.edu/rhesusgenechip/index.htm#NewRhesusGenome)
Supplementary_files_format_and_content: Read counts for animals at different timepoints (across different replicates). Format is a csv table (.csv).
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| Submission date |
Feb 09, 2022 |
| Last update date |
Feb 10, 2022 |
| Contact name |
Dan Barouch |
| Organization name |
BIDMC
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| Department |
CVVR
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| Lab |
Barouch Lab
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| Street address |
3 Blackfan Circle
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platform ID |
GPL20313 |
| Series (1) |
| GSE196436 |
Interleukin-10 regulates reservoir establishment and persistence in antiretroviral therapy-treated, SIV-infected macaques |
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| Relations |
| BioSample |
SAMN25815110 |
| SRA |
SRX14117461 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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