Skip to content

Project 1: Viral infection global analyses

Jump to bottom
Mariana G. Ferrarini edited this page Apr 7, 2020 · 11 revisions

Introduction

This wiki repository collects contributions related to the "Gene Expression" group in the COVID-19 Biohackathon April 5-11 2020. This page refers to one of the 5 projects from the Gene Expression group from the virtual BioHackathon of Covid-19 and aims at analysing RNAseq data from virus infected cells in order to detect key players in the dialogue of human and SARS-CoV-2.

A general page where you may find how the projects are related may be found here. The links to the other projects are given below:

  1. Human-viral infection analyses

  2. Risk Factors analyses

  3. Subtyping of expression response to drugs after COVID-19 infection

  4. Reporting findings to electronical medical records

Datasets

We have currently chosen three studies that compare the transcriptional response of several cell types to different viruses (with different time points and concentrations as stated below):

Study Virus Strain Cell line MOI Time (hpi)
GSE147507 SARS-CoV-2 USA-WA1/2020 NHBE 2 24 h
GSE147507 SARS-CoV-2 USA-WA1/2020 A549 0.02 24 h
GSE147507 RSV A2 A549 15 24 h
GSE147507 IAV Puerto Rico/8/1934 (H1N1) A549 5 9 h
GSE122876 MERS-CoV HCoV-EMC/2012 Calu-3 2 24 h
GSE56192 MERS-CoV HCoV-EMC/2012 MRC5 0.1 24 h
GSE56192 MERS-CoV HCoV-EMC/2012 MRC5 3 24 h
GSE56192 MERS-CoV HCoV-EMC/2012 MRC5 0.1 48 h
GSE56192 MERS-CoV HCoV-EMC/2012 MRC5 3 48 h
GSE56192 SARS Urbani strain MRC5 0.1 24 h
GSE56192 SARS Urbani strain MRC5 3 24 h
GSE56192 SARS Urbani strain MRC5 0.1 48 h
GSE56192 SARS Urbani strain MRC5 3 48 h

Methods

We analysed the previously mentioned datasets in order to compare specific responses coming from the infection of SARS-CoV-2 and filter out genes differentially expressed but rather related to general immune/viral response. This project created and followed a complete nextflow pipeline freely available for use and may be found here.

Results

Clustering of samples and PCA general analysis

Differential gene expression of primary NHBE cells infected with SARS-CoV-2

Isoform differential expression

Functional enrichment analyses

Final list of genes specific to SARS-CoV-2 infection

Clone this wiki locally