|
Status |
Public on Jul 03, 2021 |
Title |
Patient 56_Cov_D4_14 |
Sample type |
SRA |
|
|
Source name |
peripheral blood on day 4 after ICU admission
|
Organism |
Homo sapiens |
Characteristics |
subject id: Patient 56 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 |
SAMN19667065 |
SRA |
SRX11118759 |