|
| Status |
Public on May 22, 2024 |
| Title |
blood_VV003_3 mnd |
| Sample type |
SRA |
| |
|
| Source name |
blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
time: 3 mnd
genotype: WT
treatment: No treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The PAXGene Blood RNA kit (QIAGEN) was then followed for RNA isolation according to protocol
Library prep was performed using the KAPA hyperPrep kit (Roche) according to protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
VV003_103
|
| Data processing |
Read quality of the paired-end reads was assessed using FastQC (version 0.12.1). Sequencing adapters, low quality reads and low quality read ends were removed using Trim Galore (version 0.10.6), which is a wrapper around Cutadapt (version 4.3) and FastQC. Mapping and read quantification was performed with Salmon (version 1.10.1), where the human GRCh38.p14 genome was used as a reference genome with annotation provided by Ensembl.
Assembly: GRCh38.p14
Supplementary files format and content: comma separated file containing the raw counts for each sample
|
| |
|
| Submission date |
May 15, 2024 |
| Last update date |
May 22, 2024 |
| Contact name |
Jelle Maarten Blankestijn |
| Organization name |
Amsterdam UMC
|
| Street address |
meibergdreef 9
|
| City |
Amsterdam |
| ZIP/Postal code |
1105 AZ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE267625 |
Whole blood transcriptome in long-COVID patients reveals association with lung function and immune response |
|
| Relations |
| BioSample |
SAMN41413686 |
| SRA |
SRX24571583 |
