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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.
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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
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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 |