Related Experiment Video
Updated: Sep 2, 2025
Gene Expression Profiling of Infecting Microbes Using a Digital Bar-coding Platform
Published on: January 13, 2016
The current status of gene expression profilings in COVID-19 patients
Mirolyuba Ilieva1, Max Tschaikowski2, Andrea Vandin3,4
1Center for RNA Medicine, Department of Clinical Medicine Aalborg University Copenhagen Denmark.
Background:
The global pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has swept through every part of the world. Because of its impact, international efforts have been underway to identify the variants of SARS-CoV-2 by genome sequencing and to understand the gene expression changes in COVID-19 patients compared to healthy donors using RNA sequencing (RNA-seq) assay. Within the last two and half years since the emergence of SARS-CoV-2, a large number of OMICS data of COVID-19 patients have accumulated. Yet, we are still far from understanding the disease mechanism. Further, many people suffer from long-term effects of COVID-19; calling for a more systematic way to data mine the generated OMICS data, especially RNA-seq data.
Methods:
By searching gene expression omnibus (GEO) using the key terms, COVID-19 and RNA-seq, 108 GEO entries were identified. Each of these studies was manually examined to categorize the studies into bulk or single-cell RNA-seq (scRNA-seq) followed by an inspection of their original articles.
Results:
The currently available RNA-seq data were generated from various types of patients' samples, and COVID-19 related sample materials have been sequenced at the level of RNA, including whole blood, different components of blood [e.g., plasma, peripheral blood mononuclear cells (PBMCs), leukocytes, lymphocytes, monocytes, T cells], nasal swabs, and autopsy samples (e.g., lung, heart, liver, kidney). Of these, RNA-seq studies using whole blood, PBMCs, nasal swabs and autopsy/biopsy samples were reviewed to highlight the major findings from RNA-seq data analysis.
Conclusions:
Based on the bulk and scRNA-seq data analysis, severe COVID-19 patients display shifts in cell populations, especially those of leukocytes and monocytes, possibly leading to cytokine storms and immune silence. These RNA-seq data form the foundation for further gene expression analysis using samples from individuals suffering from long COVID.
Related Concept Videos
02:24Ribosome Profiling
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
01:33Proteomics
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
01:42What is Gene Expression?
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...