|
| Status |
Public on Jul 03, 2021 |
| Title |
Patient 58_Cov_D4_16 |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood on day 4 after ICU admission
|
| Organism |
Homo sapiens |
| Characteristics |
subject id: Patient 58
ifih1-rs1990760: CC
corticosteroids treatment: 0
tissue: blood
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Venous blood samples were extracted in TEMPUS tubes (Thermo Fisher). After centrifugation, pellets were homogeneized in Trizol and total RNA was extracted by isopropanol precipitation.
Amplification of known human transcripts; Libraries were prepared using the Ion Ampliseq Trascriptome Human Gene Expression Kit (Ion Torrent)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent S5 |
| |
|
| Data processing |
Basecalling was performed usin the default Ion Torrent software
trimming was performed using the fastp software v0.20.1 and the parameters -f 3, -r, -M 15
Counts were calculated using the pseudoalignment tool salmon v1.4.0 with the default parameters for mapping-based quantification and the hg38 salmon partial index
Reads were loaded in R using the tximport library
Genome_build: hg38
Supplementary_files_format_and_content: the raw count csv file was generated based on the txi matrix imported in R.
|
| |
|
| Submission date |
Jun 11, 2021 |
| Last update date |
May 27, 2023 |
| Contact name |
Guillermo M Albaiceta |
| E-mail(s) |
gma@crit-lab.org
|
| Phone |
+34 985 652433
|
| Organization name |
Instituto de Investigación Sanitaria del Principado de Asturias
|
| Lab |
Laboratorio de Investigación Traslacional en el paciente crítico
|
| Street address |
Avenida de Roma s/n
|
| City |
Oviedo |
| ZIP/Postal code |
33011 |
| Country |
Spain |
| |
|
| Platform ID |
GPL23934 |
| Series (1) |
| GSE177025 |
Effects of steroids on peripheral blood gene expression in COVID-19 patients according to rs1990760 variants |
|
| Relations |
| Reanalyzed by |
GSE233627 |
| BioSample |
SAMN19667085 |
| SRA |
SRX11118761 |
