|
| Status |
Public on May 05, 2024 |
| Title |
PBMC, NoDex, patient 50, bulkRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: PBMC
disease state: severely ill COVID-19 patient
study days: 0
treatment: NoDex
|
| Treatment protocol |
The Dex group received at least one dose of 6mg dexamethasone at the time of initial biosampling
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from 2.5 x 105 PBMCs using the Quick-RNA MagBead Kit (Zymo) with DNase digestion
RNA quality was assessed using a Fragment Analyzer (Agilent) and 10ng RNA was used to synthesize full length cDNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio). The cDNA was purified using bead cleanup, followed by library preparation. Libraries were validated on a Fragment Analyzer (Agilent), pooled at equimolar concentrations, and sequenced on an Illumina NovaSeq6000 (Emory) at 100 bp paired-end read length targeting ~25 million reads per sample. using Nextera XT kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
MVIR1-HS50-D0PBMC1-RSQ2
|
| Data processing |
Gene counts were generated using the nf-core rnaseq pipeline v3.3
Salmon-generated counts were used for analysis
Assembly: GRCh38
Supplementary files format and content: CSV file including Salmon-generated raw counts
|
| |
|
| Submission date |
Jul 11, 2023 |
| Last update date |
May 05, 2024 |
| Contact name |
Ravi Patel |
| E-mail(s) |
ravi.patel2@ucsf.edu
|
| Organization name |
University of California San Francisco
|
| Department |
CoLabs
|
| Lab |
Fragiadakis lab
|
| Street address |
513 Parnassus Ave
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE237109 |
Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19 |
| GSE237180 |
Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19. |
|
| Relations |
| BioSample |
SAMN36409192 |
| SRA |
SRX20989121 |
