{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Giulia Soldà"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15584"],"description":["To identify possible deregulated pathways involved in COVID-19 severity, we analyzed the transcriptomic profiles of 59 patients affected by severe COVID-19 symptoms, comparing those who were only hospitalized and required supplemental oxygen support (N=24) with those who were also admitted to the ICU and received more intensive respiratory support, such as non-invasive ventilation or ventilator support (N=35, critically severe)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Blood samples were collected in 4 mL ethylene-diaminetetraacetic acid-K2 vacuum blood tubes, mixed immediately after the collection by inverting 10 times, and processed less than 8 hours after the blood withdrawal. Peripheral blood mononuclear cells (PBMCs) isolation was performed by using Ficoll (Sigma-Aldrich, St. Louis, Missouri, USA) density gradient centrifugation.","Library Construction - Libraries were prepared from 35-57 ng of total RNA, using the SMARTer Stranded RNA-Seq Kit (Clontech-Takara, Kusatsu, Shiga, Japan), following the manufacturer's instructions.","Sequencing - Libraries from 59 samples were multiplexed in two different equimolar pools and sequenced in two separate runs on a NextSeq 2000 Platform (Illumina; Illumina, San Diego, California, USA) generating paired-end 150-nucleotide reads.","Nucleic Acid Extraction - Total RNA was isolated from PBMCs using the TriFast reagent (Euroclone, Pero, Milan, Italy). For assessing RNA quantity and quality we used a highly sensitive fluorescence-based quantitation system (Qubit HSRNA; Thermo Fisher Scientific, Waltham, Massachusetts, USA) and the High Sensitivity RNA ScreenTape Assay with a 4200 Tapestation System (Agilent Technologies, Santa Clara, California, USA)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Quantification of reads mapping on each protein coding gene was obtained with STAR v2.7.9a (Spliced Transcripts Alignment to a Reference) using the command “--quantMode GeneCounts” and the UCSC transcript annotation.","Sequence Alignment - Mapping and quantification of RNA-seq reads were performed on the hg38 reference human genome (UCSC) using STAR (v2.7.9a)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"pubmed_abstract":["<h4>Background</h4>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected over 26 million individuals in Italy, resulting in ∼200,000 COVID-19-related deaths. Unravelling host genetic factors underlying disease severity is key to understanding progression mechanisms.<h4>Methods</h4>We applied multi-omics approaches to investigate genetic susceptibility to COVID-19 severity in the Italian population. We combined an exome-wide case-control study of rare germline variants (215 severe/critically ill patients vs 1755 controls) with transcriptomic (differential gene expression and alternative splicing) analyses of 59 hospitalised patients to identify signatures associated with severe respiratory outcomes (ICU admission).<h4>Findings</h4>Rare variant analysis revealed significant a"],"study_type":["RNA-seq of total RNA"],"species":["Homo sapiens"],"pubmed_title":["Multi-omics identifies oxidative stress, prothrombotic pathways, and lactoperoxidase variants as key factors in COVID-19 severity"],"pubmed_authors":["Rosanna Asselta","Claudio Cappadona, Valeria Rimoldi, Francesca Tettamanzi, Giulia Cardamone, Alberto Mantovani, Giulia Soldà,  Elvezia Maria Paraboschi, Rosanna Asselta","Giulia Soldà"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of human Peripheral blood mononuclear cells (PBMCs) from COVID-19 patients requiring different degree of respiratory support","description":"To identify possible deregulated pathways involved in COVID-19 severity, we analyzed the transcriptomic profiles of 59 patients affected by severe COVID-19 symptoms, comparing those who were only hospitalized and required supplemental oxygen support (N=24) with those who were also admitted to the ICU and received more intensive respiratory support, such as non-invasive ventilation or ventilator support (N=35, critically severe).","dates":{"release":"2026-07-20T00:00:00Z","modification":"2026-09-07T12:10:14.139Z","creation":"2025-09-12T12:01:17.284Z"},"accession":"E-MTAB-15584","cross_references":{"pubmed":["41500120"],"ENA":["ERP180013"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"],"doi":["10.1016/j.ebiom.2025.106111"]}}