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Sample GSM8224826 Query DataSets for GSM8224826
Status Public on May 10, 2024
Title 10-7_RhDFRi_SIV_CD8N
Sample type SRA
 
Source name peripheral blood
Organism Macaca mulatta
Characteristics tissue: peripheral blood
cell type: CD8 naiveT cell
disease state: SIV
Extracted molecule polyA RNA
Extraction protocol RNA was extracted from pelleted cells resuspended in Buffer RLT Plus (Qiagen) with 1% BME. RNA was extracted using RNeasy Micro kit (Qiagen).
SMART-Seq® v4 Ultra® Low Input RNA was used for mRNA library preparation.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing RNA-seq samples were sequenced as 101bp paired-end libraries on a Novaseq S4. All samples had over 109 million reads.
Reads were trimmed using Cutadapt (v1.18) and aligned to the Mmul_10/RheMac10 reference genome and Gencode (Ensembl release 108) using STAR (v2.7.6a) in 2-pass basic mode. Expression levels were quantified with RSEM (v1.3.3) before being converted into FPKM values.
Assembly: RheMac10
Supplementary files format and content: SIV.RawCountFile_rsemgenes.txt: tab-delimited raw counts for each sample
Supplementary files format and content: SIV.FPKM.all_samples.txt: tab-delimited FPKM values for each sample
 
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
 
Platform ID GPL27943
Series (1)
GSE264657 SIV infection and ARV treatment reshape the transcriptional and epigenetic profile of naïve and memory T cells in vivo (RNA-Seq)
Relations
BioSample SAMN41059837
SRA SRX24345754

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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