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| Status |
Public on Jul 23, 2014 |
| Title |
AV21_PBMC_Uninf_D10 |
| Sample type |
SRA |
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| Source name |
PBMC
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| Organism |
Macaca mulatta |
| Characteristics |
animal id: AV21
treatment group: Uninf
day post infection: D10
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from samples using RNAzol RT and was enriched for polyadenylated transcripts by hybridization with oligo-dT(25) magnetic beads.
Enriched polyadenylated RNA was fragmented randomly with heat and divalent cations, and reverse-transcribed from random hexamer primers. Second strand synthesis was then performed using RNAse-H and DNA Polymerase I. Double-stranded cDNA was end repaired and A-tailed, and then ligated to a hairpin-loop sequencing adaptor (New England Biolabs). Libraries were then enriched and barcoded by PCR, validated on a Bioanalyzer, and quantified by qPCR. Individually libraries were then pooled and quantified again before cluster generation and sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
s_5_1_18_130607_SN622_0225_AD1DWLACXX
processed data file: Acute_PBMC_Uninfected_FPKM_exprs.txt
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| Data processing |
RNA-Seq data were aligned to a provisional assembly of Indian Macaca mulatta (MuSuRCA rhesus assembly v.4) using STAR version 2.3.0e. {Dobin 2012}; parameters were set using the annotation as a splice junction reference, un-annotated non-canonical splice junction mappings and non-unique mappings were removed from downstream analysis.
Transcripts were annotated using the provisional UNMC annotation v4.12 Norgren Accession pending. Transcript assembly, abundance estimates, and differential expression analysis was performed using Cufflinks v2.1.1 and Cuffdiff 2{Trapnell 2013}.
Group 1 was comprised of 166 samples and contained the samples from PBMCs from the saline+SIV, IFN-1ant+SIV, and pegylated IFN_2a-treated+SIV animals, and from samples for the analysis of PBMCS, LN CD4+ T cells and rectal biopsies of uninfected, IFNa treated animals; the average number of mapped reads was 12,188,890 (range: 3,237,374-87,371,564).
Group 2 was comprised of the LN CD4 T cells from the three SIV-infected groups consisting of 37 samples, the average mapped read count for this group was 4,898,448 (range: 1,173,455-19,310,483).
Genome_build: MuSuRCA rhesus assembly v.4
Supplementary_files_format_and_content: Tab delimited text with rows of transcript ID's and columns of sample ID's and sample FPKMs
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| Submission date |
Dec 27, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Gregory K Tharp |
| E-mail(s) |
gktharp@emory.edu
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| Phone |
404-727-7797
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| Organization name |
Yerkes National Primate Research Center
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| Department |
Developmental and Cognitive Neuroscience
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| Lab |
Genomics Core
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| Street address |
954 Gatewood Dr
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| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30329-4208 |
| Country |
USA |
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| Platform ID |
GPL14954 |
| Series (1) |
| GSE53690 |
Type I IFN responses in rhesus macaques prevent SIV transmission and slow disease progression |
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| Relations |
| SRA |
SRX393332 |
| BioSample |
SAMN02486822 |
| 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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