Analysis workflow of publicly available RNA-sequencing datasets

Pablo Sanchis; Rosario Lavignolle; Mercedes Abbate; Sofía Lage-Vickers; Elba Vazquez; Javier Cotignola; Juan Bizzotto; Geraldine Gueron

doi:10.1016/j.xpro.2021.100478

Analysis workflow of publicly available RNA-sequencing datasets

STAR Protoc. 2021 Jun 18;2(2):100478. doi: 10.1016/j.xpro.2021.100478. Epub 2021 Apr 22.

Authors

Pablo Sanchis^{1

2}, Rosario Lavignolle^{1

2}, Mercedes Abbate^{1

2}, Sofía Lage-Vickers^{1

2}, Elba Vazquez^{1

2}, Javier Cotignola^{1

2}, Juan Bizzotto^{1

2}, Geraldine Gueron^{1

2}

Affiliations

¹ Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Buenos Aires C1428EGA, Argentina.
² CONICET - Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires C1428EGA, Argentina.

Abstract

Differential gene expression analysis is widely used to study changes in gene expression profiles between two or more groups of samples (e.g., physiological versus pathological conditions, pre-treatment versus post-treatment, and infected versus non-infected tissues). This protocol aims to identify gene expression changes in a pre-selected set of genes associated with severe acute respiratory syndrome coronavirus 2 viral infection and host cell antiviral response, as well as subsequent gene expression association with phenotypic features using samples deposited in public repositories. For complete details on the use and outcome of this informatics analysis, please refer to Bizzotto et al. (2020).

Keywords: Bioinformatics; RNAseq.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19 / genetics*
COVID-19 / virology
Exome Sequencing
Humans
RNA, Viral / analysis
RNA, Viral / genetics*
SARS-CoV-2 / genetics
SARS-CoV-2 / isolation & purification*
Sequence Analysis, RNA / methods*
Transcriptome*
Workflow*

Substances

RNA, Viral