|
| Status |
Public on Dec 01, 2023 |
| Title |
SA-3 |
| Sample type |
SRA |
| |
|
| Source name |
PBMC
|
| Organism |
Macaca mulatta |
| Characteristics |
tissue: PBMC
treatment: Beta infection
time: 7dpi
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from sample using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.
digital RNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-T7 |
| |
|
| Description |
SA_3RPKM
|
| Data processing |
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
The de-duplicated consensus sequences were used for standard RNA-seq analysis. They were mapped to the reference genome of macaca mulatta from Mmul_8.0 using STAR software (version 2.5.3a) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor)
Assembly: Mmul_8.0
|
| |
|
| Submission date |
Nov 03, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Lin dongdong |
| E-mail(s) |
Dongdong0216@student.pumc.edu.cn
|
| Phone |
18256786026
|
| Organization name |
Peking Union Medical College
|
| Street address |
云南省昆明市五华区茭菱路
|
| City |
昆明市 |
| State/province |
云南 |
| ZIP/Postal code |
650032 |
| Country |
China |
| |
|
| Platform ID |
GPL33913 |
| Series (1) |
| GSE246985 |
The transcriptomic landscape of PBMC in SARS-CoV-2 variants-infected Rhesus monkeys via digital RNA-seq analysis |
|
| Relations |
| BioSample |
SAMN38092029 |
| SRA |
SRX22366309 |
