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. 2024 Jan 31;19(1):e0297664. doi: 10.1371/journal.pone.0297664

Table 1. Summary of RNA sequence sample sets of COVID-19 in Gene Expression Omnibus.

GEO accession GSE title Tissue Platform Sample size
GSE152075 In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age [31] Nasopharyngeal swab GPL18573 Illumina NextSeq 500 (Homo sapiens) 484
(COVID: control = 430: 54)
GSE152075 Summary

  1. SARS-CoV-2 triggered an antiviral response driven by interferon and concurrently decreased the transcription of ribosomal proteins. Levels of B cells and neutrophils were higher in patients with a lower viral load.

  2. A decrease in the expression of chemokines CXCL9/10/11, cognate receptors CXCR3, CD8A, and granzyme B was observed in elderly individuals.

  3. B- and NK-cell-specific transcripts were reduced and NF-κB inhibitors increased in males.
GSE163151 A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood [32] Nasopharyngeal swab GPL24676 Illumina NovaSeq 6000 (Homo sapiens) 149
(COVID: control = 138: 11)
GSE163151 Summary

  1. A two-step classifier based on machine learning that was run on an individual test set of NP swab samples was able to segregate COVID-19 and non-COVID-19 and infectious or noninfectious acute respiratory disease with 85.1%-86.5% accuracy.

  2. SARS-CoV-2 infection has unique biologic features and differences between NP swabs and whole blood that can be used in the differential diagnosis of COVID-19.
GSE169241 hPSC-derived cells to model macrophage-mediated inflammation in COVID-19 Hearts [33] Human heart autopsy tissues GPL24676 Illumina NovaSeq 6000 (Homo sapiens) 8
(COVID: control = 3:5)
GSE169241 Summary

  1. COVID-19 patients showed a significant increase in CCL2 expression and macrophage infiltration in cardiac tissue.

  2. After SARS-CoV-2 exposure, macrophages induced increased cardiomyocyte reactive oxygen species and apoptosis via secretion of IL-6 and TNF-α.
GSE157103 Large-scale multiomic analysis of COVID-19 severity [34] Leukocyte GPL24676 Illumina NovaSeq 6000 (Homo sapiens) 126
(COVID: control = 100: 26;
ICU: non-ICU = 50: 50)
GSE157103 Summary

  1. Coagulation-related proteins, as well as cellular fibronectin (cFN), were significantly increased in COVID-19 patients.

  2. The abundance of prothrombin, which is cleaved to form thrombin during coagulation, was significantly reduced and correlated with severity, which may help to elucidate the hypercoagulable environment of SARS-CoV-2 infection.
GSE152641 Transcriptomic similarities and differences in host response between SARS-CoV-2 and other viral infection [35] Whole blood GPL24676 Illumina NovaSeq 6000 (Homo sapiens) 86
(COVID: control = 62: 24)
GSE152641 Summary

  1. Changes in gene expression in the peripheral blood of COVID-19 patients correlated highly with changes in response to other viral infections. However, two genes, ACO1 and ATL3, showed significantly different changes in expression.

  2. Some dynamic immune evasion and counter host responses are specific to COVID-19. For example, CD56bright NK cells, M2 macrophages, and total NK cells were increased in COVID-19.