{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T22:22:13Z","timestamp":1788819733420,"version":"build-2803163510"},"reference-count":29,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2022,7,17]],"date-time":"2022-07-17T00:00:00Z","timestamp":1658016000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Clinical and Translational Dis"],"published-print":{"date-parts":[[2022,9]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>The global pandemic of coronavirus disease 2019 (COVID\u201019) caused by severe acute respiratory syndrome coronavirus 2 (SARS\u2010CoV\u20102) has swept through every part of the world. Because of its impact, international efforts have been underway to identify the variants of SARS\u2010CoV\u20102 by genome sequencing and to understand the gene expression changes in COVID\u201019 patients compared to healthy donors using RNA sequencing (RNA\u2010seq) assay. Within the last two and half years since the emergence of SARS\u2010CoV\u20102, a large number of OMICS data of COVID\u201019 patients have accumulated. Yet, we are still far from understanding the disease mechanism. Further, many people suffer from long\u2010term effects of COVID\u201019; calling for a more systematic way to data mine the generated OMICS data, especially RNA\u2010seq data.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>By searching gene expression omnibus (GEO) using the key terms, COVID\u201019 and RNA\u2010seq, 108 GEO entries were identified. Each of these studies was manually examined to categorize the studies into bulk or single\u2010cell RNA\u2010seq (scRNA\u2010seq) followed by an inspection of their original articles.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The currently available RNA\u2010seq data were generated from various types of patients\u2019 samples, and COVID\u201019 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\u2010seq studies using whole blood, PBMCs, nasal swabs and autopsy\/biopsy samples were reviewed to highlight the major findings from RNA\u2010seq data analysis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Based on the bulk and scRNA\u2010seq data analysis, severe COVID\u201019 patients display shifts in cell populations, especially those of leukocytes and monocytes, possibly leading to cytokine storms and immune silence. These RNA\u2010seq data form the foundation for further gene expression analysis using samples from individuals suffering from long COVID.<\/jats:p><\/jats:sec>","DOI":"10.1002\/ctd2.104","type":"journal-article","created":{"date-parts":[[2022,7,17]],"date-time":"2022-07-17T16:08:45Z","timestamp":1658074125000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["The current status of gene expression profilings in COVID\u201019 patients"],"prefix":"10.1002","volume":"2","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7992-8885","authenticated-orcid":false,"given":"Mirolyuba","family":"Ilieva","sequence":"first","affiliation":[{"name":"Center for RNA Medicine, Department of Clinical Medicine Aalborg University  Copenhagen Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Max","family":"Tschaikowski","sequence":"additional","affiliation":[{"name":"Department of Computer Science Aalborg University  Aalborg Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea","family":"Vandin","sequence":"additional","affiliation":[{"name":"Institute of Economics and EMbeDS Sant'Anna School of Advanced Studies  Pisa Italy"},{"name":"Department of Applied Mathematics and Computer Science Technical University of Denmark  Kongens Lyngby Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4787-8067","authenticated-orcid":false,"given":"Shizuka","family":"Uchida","sequence":"additional","affiliation":[{"name":"Center for RNA Medicine, Department of Clinical Medicine Aalborg University  Copenhagen Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2022,7,17]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evab196"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.metabol.2020.154262"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1183\/23120541.00542\u20102020"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.7759\/cureus.9540"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.08.028"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms10030598"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/S1473\u20103099(22)00296\u20101"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2021.102711"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.abj7521"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.821730"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13223\u2010019\u20100382\u2010x"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1007\/7651_2014_99"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.812514"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0254066"},{"key":"e_1_2_10_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.medj.2021.04.008"},{"key":"e_1_2_10_17_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010020\u201017834\u2010w"},{"key":"e_1_2_10_18_1","doi-asserted-by":"publisher","DOI":"10.1002\/ctm2.534"},{"key":"e_1_2_10_19_1","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abe5984"},{"key":"e_1_2_10_20_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.824967"},{"key":"e_1_2_10_21_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010021\u201003570\u20108"},{"key":"e_1_2_10_22_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010021\u201027723\u20105"},{"key":"e_1_2_10_23_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajpath.2021.08.009"},{"key":"e_1_2_10_24_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010020\u201020139\u20107"},{"key":"e_1_2_10_25_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010021\u201021702\u20106"},{"key":"e_1_2_10_26_1","doi-asserted-by":"publisher","DOI":"10.1016\/S2213\u20102600(22)00126\u20106"},{"key":"e_1_2_10_27_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.xpro.2021.100873"},{"key":"e_1_2_10_28_1","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2021.656433"},{"key":"e_1_2_10_29_1","doi-asserted-by":"publisher","DOI":"10.3389\/fcvm.2020.623012"},{"key":"e_1_2_10_30_1","doi-asserted-by":"publisher","DOI":"10.3892\/ijmm.2020.4702"}],"container-title":["Clinical and Translational Discovery"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/ctd2.104","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/ctd2.104","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/ctd2.104","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,19]],"date-time":"2023-08-19T21:17:50Z","timestamp":1692479870000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/ctd2.104"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,7,17]]},"references-count":29,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2022,9]]}},"alternative-id":["10.1002\/ctd2.104"],"URL":"https:\/\/doi.org\/10.1002\/ctd2.104","archive":["Portico"],"relation":{},"ISSN":["2768-0622","2768-0622"],"issn-type":[{"value":"2768-0622","type":"print"},{"value":"2768-0622","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,7,17]]},"assertion":[{"value":"2022-06-01","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2022-06-19","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2022-07-17","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e104"}}