|
| Status |
Public on Dec 23, 2022 |
| Title |
Blood sample from COVID-19 patient P2 at day 7 |
| Sample type |
SRA |
| |
|
| Source name |
Blood sample
|
| Organism |
Homo sapiens |
| Characteristics |
individual: patient P2
infection: SARS-CoV2
treatment: anakinra
time: day 7
tissue: Whole blood
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted with Paxgene ® Blood RNA Kit (Qiagen, Hilden, Germany).
Poly-A enriched libraries were generated with Illumina TruSeq mRNA Stranded kit according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
P2_day7
|
| Data processing |
Basecalling was performed using bcl2fastq version 2.20.0.
Reads were trimmed for low-quality ends with TrimGalore version 0.6.6
Reads were aligned to the hg38 reference transcriptome and transcript abundance was estimated with Kallisto version 0.43.
Kallisto counts were normalized by the regularized log (rlog) transformation using the DeSeq2 R Package
Genome_build: hg38
Supplementary_files_format_and_content: Comma-delimited text files include rlog values for each sample and time point
|
| |
|
| Submission date |
Dec 16, 2020 |
| Last update date |
Dec 23, 2022 |
| Contact name |
Paolo Uva |
| Organization name |
IRCCS Istituto Giannina Gaslini
|
| Lab |
Clinical Bioinformatics
|
| Street address |
Via Gerolamo Gaslini, 5
|
| City |
Genoa |
| ZIP/Postal code |
16147 |
| Country |
Italy |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE163317 |
Spontaneous NLRP3 inflammasome-driven IL-1-β secretion is induced in severe COVID-19 patients and responds to anakinra treatment |
|
| Relations |
| BioSample |
SAMN17091832 |
| SRA |
SRX9690464 |
