|
| Status |
Public on Mar 09, 2021 |
| Title |
COV4: COVID sample 4 |
| Sample type |
SRA |
| |
|
| Source name |
Frontal cortex
|
| Organism |
Homo sapiens |
| Characteristics |
disease: COVID-19
dementia status: No Dementia
tissue: Frontal cortex
|
| Growth protocol |
Autoptic human brain samples were collected. Slices of anterior frontal lobe were fresh cut into about 10 mm thickness and frozen at -80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were homogenized and total RNA was isolated by Trizol® reagent (Life Science Technologies, Italy) following the manufacturer’s specifications. RNAs were quantified using a Nanodrop ND-100 Spectrophotometer (Nanodrop Technologies, Wilmington, USA) and a 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit, Waldbronn, Germany); RNAs with a 260:280 ratio of ≥1.5 and an RNA integrity number of ≥8 were subjected to deep sequencing.
Sequencing libraries were prepared by the Lexogen CORALL Total RNA-Seq Library Prep Kit using 500-ng total RNA (Lexogen). Qualities of sequencing libraries were assessed with 4200 TapeStation with the DNA1000 reagent kit. RNA processing has been carried out using Illumina NextSeq 500 Sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
COV4
|
| Data processing |
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Gene and transcript intensities were computed using STAR/RSEM software using Gencode Release m24 (GRCm38) as a reference, using the “-strandness forward” option. Differential expression analysis for mRNA and lncRNA was performed using R package DESeq2
Genome_build: HG19
|
| |
|
| Submission date |
Jan 06, 2021 |
| Last update date |
Sep 07, 2021 |
| Contact name |
Maria Garofalo |
| E-mail(s) |
maria.garofalo01@universitadipavia.it
|
| Organization name |
IRCCS Mondino Foundation
|
| Lab |
Genomic and Post Genomic Unit
|
| Street address |
Via Mondino 2
|
| City |
Pavia |
| ZIP/Postal code |
27100 |
| Country |
Italy |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE164332 |
Frontal Cortex whole transcriptome sequencing in COVID-19 elderly patients |
|
| Relations |
| BioSample |
SAMN17226582 |
| SRA |
SRX9791270 |
