Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species

PRJNA741686: Baseline signatures associated with clinical, virologic, and immunologic outcomes in patients with mild to moderate COVID-19

Source: NCBI / GSE178967
Submission Date: Jun 26 2021
Release Date:
Update Date: Oct 01 2021

Summary: The vast majority of SARS-CoV-2 infections are uncomplicated and do not require hospitalization, but these infections contribute to ongoing transmission. There remains a critical need to identify host immune biomarkers predictive of virologic and clinical outcomes in planning future treatment studies of COVID-19. We recently completed a randomized clinical trial of Pegylated PegIinterferon Lambda for treatment of SARS-CoV-2 infected patients conducted in the Stanford COVID-19 CTRU. Leveraging longitudinal samples and data from this trial, we define early immunebaseline and infection-induced signatures that predict the duration of viral shedding, resolution of symptoms, and immunologic memory.

Overall Design: We recruited 108 subjects between age 18 to 75 who are PCR positive for SARS-CoV-2. The subjects were randomized to receive a single dose of Peginterferon Lambda or placebo at their first visit (day 0). In-person follow-up visits were conducted on Day 1, 3, 5, 7, 10, 14, 21, and 28, with the assessment of symptoms and vitals and collection of oropharyngeal swabs for SARS-CoV-2 testing. To profile the immune response in the COVID-19 patients, we conducted RNA-sequencing assays using blood samples collected at day 0 and day 5 after enrollment.

GEN Datasets:
GEND000377
Strategy:
Species:
Tissue:
Healthy Condition:
Protocol
Growth Protocol: -
Treatment Protocol: -
Extract Protocol: First the samples were treated with Proteinase K, and then some extractions were performed using Quick-RNA MagBead Kit (R2132) on KingFisher.
Library Construction Protocol: Libraries were prepared using ZymoSeq RiboFree Total RNA Library Kit (R3000).
Sequencing
Molecule Type: rRNA- RNA
Library Source:
Library Layout: PAIRED
Library Strand: Forward; -
Platform: ILLUMINA
Instrument Model: Illumina NovaSeq 6000
Strand-Specific: Specific; Unspecific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Publications
Early immune responses have long-term associations with clinical, virologic, and immunologic outcomes in patients with COVID-19.
Research square . 2022-02-02 [PMID: 35132407]