|
| Status |
Public on Feb 28, 2022 |
| Title |
miRNA4 |
| Sample type |
SRA |
| |
|
| Source name |
serum sample
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
disease: COVID-19
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Venous blood samples were extracted, centrifugued and serum was homogeneized with TRIzol (Thermo Fisher). miRNA was extracted using the miRNeasy kit (Quiagen).
Library construction and sequencing was externalized to BGI Genomics (Beijin, China)
Standard BGI protocol for miRNA sequencing was applied
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
DNBSEQ-T7 |
| |
|
| Data processing |
Basecalling was performed using the default Illumina software
trimming was performed using the trim_galore software v0.6.6 and the parameters -length 16
mapping was performed using the miRDeep2 mapper.pl script (last update 21/04/2016). A bowtie index for hg38 was used.
known and novel miRNAs were quantified using the miRDeep2.pl script v2.0.1.3. Mature and hairpin human miRNA sequences were downloaded from miRBase. MiRNAs annotated for all primate species were used as reference for the discovery step.
Genome_build: hg38
Supplementary_files_format_and_content: the csv file is the direct output from the miRDeep script
Supplementary_files_format_and_content: Raw counts and normalized counts
|
| |
|
| Submission date |
Feb 23, 2022 |
| Last update date |
Feb 28, 2022 |
| Contact name |
Guillermo M Albaiceta |
| E-mail(s) |
[email protected]
|
| 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 |
GPL29480 |
| Series (2) |
| GSE197258 |
Transcriptomic clustering of critically-ill COVID-19 patients [Day 1-miRNA-Seq] |
| GSE197259 |
Transcriptomic clustering of critically-ill COVID-19 patients |
|
| Relations |
| BioSample |
SAMN26195975 |
| SRA |
SRX14260710 |
