In this blog post, we summarize all curated data on coronaviruses available in GENEVESTIGATOR®. In a recent effort to assist research on the topic of coronaviruses amid the current COVID-19 pandemic, we have curated 61 studies with 4437 samples from human and mouse (Figure 1). The studies can be explored in GENEVESTIGATOR® under Data Selection/New/Search by keyword: “Coronavirus”.
DISTRIBUTION BY SPECIES
Figure 1: Distribution of curated studies on coronaviruses and their samples by species. The distribution of studies is shown on the left, and the distribution of samples on the right.
DISTRIBUTION BY STUDY TYPE
The curated studies can be further classified based on the global study type (Figure 2), whereby more studies were performed in vitro compared to in vivo, and a few studies included both study types. No ex vivo studies were included.
Figure 2: Distribution of curated studies on coronaviruses by global study type.
DISTRIBUTION BY STUDY DESIGN
The curated studies included multiple study designs (Figure 3), whereby the majority are classified as pathogenicity studies. Pathogenicity and time series studies mainly constitute in vitro studies investigating the effect of various coronavirus strains and doses in different tissue culture settings. Compound treatment studies include several tested compounds, including, but not limited to, amlodipine, berbamine, camostat, loperamide, imatinib, and ruxolitinib. Disease state studies include comparisons of mild vs. moderate vs. severe and critical COVID-19 cases, in addition to comparisons of low vs. high viral load.
Figure 3: Distribution of curated studies on coronaviruses by study design.
DISTRIBUTION BY STUDY TOPIC
In terms of the main topic of the study, most studies investigated SARS-CoV-2, followed closely by studies with samples from SARS-CoV-2 infected patients (i.e., COVID-19 patients). Figure 4 shows the distribution of the curated studies by main topic of study.
Figure 4: Distribution of curated studies on coronaviruses by main topic of study.
DISTRIBUTION BY ANATOMY
The 51 human studies include samples from 38 different anatomies – tissue, cell type, 3D culture – of which the top 5 with the largest number of samples are highlighted in Table 1.
Table 1: Top 5 anatomies – tissue, cell type, and 3D culture - with largest number of samples. Selection: All HS platforms.
DISTRIBUTION BY CELL LINE
The 51 human studies also included samples from 24 different cell lines. The top 5 cell lines with the largest number of samples are highlighted in Table 2.
Table 2: Top 5 cell lines with largest number of samples. Selection: All HS platforms.
COVID-19 SINGLE-CELL DATA
The three human studies with single-cell RNA-Seq study design available in GENEVESTIGATOR® can be found on the ‘aggregate 10x single-cell RNA-Seq Gene Level Homo sapiens’ platform (Table 3). Data from droplet-based libraries are featured as 1 sample = 1 aggregate, where an aggregate is a group of cells from the same biosample that have shared attributes, e.g., cell type and cell state. All users with a valid GENEVESTIGATOR® license get full access to one COVID-19 study (HS-03428/GSE145926). For a detailed example analysis of this 10x single-cell RNA-Seq dataset on the topic of COVID-19, see here. For more information on the two free data sets, see here.
Table 3: List of single-cell RNA-Seq curated studies on coronaviruses available in GENEVESTIGATOR®. Selection: aggregate 10x single-cell RNA-Seq Gene Level Homo sapiens. GV stands for GENEVESTIGATOR®.
For more information on the curated studies on coronaviruses and for comprehensive lists (Tables 1-2), contact us at firstname.lastname@example.org.