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Sample GSM7158690 Query DataSets for GSM7158690
Status Public on Dec 06, 2023
Title 80B_14954_24W_PBMC
Sample type SRA
 
Source name Peripheral blood mononuclear cells
Organism Macaca mulatta
Characteristics cell type: Peripheral blood mononuclear cells
set: B
subjectid: 14954
sivgenotype: {delta}vpr
infection status: 24W
timepoint (weeks): 24W
Extracted molecule total RNA
Extraction 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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description Δvpr
Data processing The sequencing data was demultiplexed using Illumina bcl2fastq v2.20.0.422.
The quality of raw reads was assessed with FastQC v0.11.8.
Reads were mapped to the Rhesus macaque (MacaM v7) genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the htseq-count algorithm.
Assembly: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf,https://www.unmc.edu/rhesusgenechip/index.htm#Rhesus)
Supplementary files format and content: tab delimited text file containing raw read counts for each sample (in columns) and each annotated transcript (in rows).
 
Submission date Apr 10, 2023
Last update date Dec 06, 2023
Contact name Gregory K Tharp
E-mail(s) gktharp@emory.edu
Phone 404-727-7797
Organization name Yerkes National Primate Research Center
Department Developmental and Cognitive Neuroscience
Lab Genomics Core
Street address 954 Gatewood Dr
City Atlanta
State/province GA
ZIP/Postal code 30329-4208
Country USA
 
Platform ID GPL23804
Series (1)
GSE229310 Vpr attenuates antiviral immune responses and is critical for full pathogenicity of SIVmac239 in rhesus macaques
Relations
SRA SRX19918966
BioSample SAMN34130400

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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