|
| Status |
Public on May 10, 2024 |
| Title |
3-3_A0P031_SIV_CD8N |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood
|
| Organism |
Macaca nemestrina |
| 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 |
GPL33261 |
| 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 |
SAMN41059925 |
| SRA |
SRX24345666 |
