{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Theodoros Simakou"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14405"],"description":["The data here represent two Single-Cell experiments performed to understand the roles of PROS1 in bronchial epithelial cells and monocytes, infected by SARS-CoV-2. The CVR EXP5 contains epithelial cultures grown on Air-Liquid Interface as mock or infected by the delta variant of SARS-CoV-2 (Delta B.1.617.2), and cocultures of mock or infected epithelium with CD14 monocytes. Some of these cultures were also supplemented with PROS1, to study the effects of the protein during infection. The CVR EXP1 contains cultures of PBMCs cultured in presence of SARS-CoV-2 variant (BetaCoV/England/02/2020/EPI_ISL_407073 ), with or without PROS1 supplementation. CVR EXP5 libraries were prepared using the Whole transcriptome Analysis and Sample Tag library Preparation kit (BD 633801), as per manufacture’s protocol (2019 version). CVR EXP1 libraries of 399 genes were prepared using BD Rhapsody Targeted mRNA and the Tag Amplification Kit (no. 633774) and primers from the BD Rhapsody Immune response Panel Hs (399 genes, BD 633750), as per manufacture’s protocol."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - cDNA was synthesised on mRNA captured on the beads using BD Rhapsody cDNA Kit (Cat. No. 633773), following manufacture’s protocol. Libraries of 399 genes (CVR EXP1) were prepared using BD Rhapsody Targeted mRNA and the Tag Amplification Kit (no. 633774) and primers from the BD Rhapsody Immune response Panel Hs (399 genes, BD 633750), as per manufacture’s protocol.  Whole transcriptome libraries (CVR EXP5) were prepared using the Whole transcriptome Analysis and Sample Tag library Preparation kit (BD 633801), as per manufacture’s protocol (2019 version).","Nucleic Acid Extraction - The cells were then tagged in FACS buffer using the BD Human multiplex tags (BD, 633781). After the incubation, the cells were washed three times, pooled together, and loaded onto the scRNA-seq BD Rhapsody Cartridge of single-cell RNA extraction, using the BD Rhapsody Cartridge Reagent Kit (no. 633731) according to the manufacturer’s protocol.","Sequencing - Libraries were sequenced using Illumina NextSeq 500","Sample Collection - On the days of the extraction, the cells were washed with D-PBS, which was collected in individual tubes. Then the cells were lifted using Triple Express (Gibco, 12604-013) for 15 minutes at 37oC. The cell suspension was then transferred into the respective tubes, and the transwells were washed once with D-PBS to collect all the cells. The dead cells were then removed using the EasySep™ Dead Cell Removal (Annexin V) Kit (StemCell Technologies, 17899) as described in manufacturer’s protocol, with the only difference that the cells were collected in 2 mL polypropylene tubes (Sarstedt, 72693) and live cells were negatively separated using DynaMag2 magnet (Life technologies, 12321D), in order to avoid pouring of suspensions while working with the virus.  The cells were then tagged in FACS buffer using the BD Human multiplex tags (BD, 633781). After the incubation, the cells were washed three times, pooled together, and loaded onto the scRNA-seq BD Rhapsody Cartridge of single-cell RNA extraction, using the BD Rhapsody Cartridge Reagent Kit (no. 633731) according to the manufacturer’s protocol."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Mapping was performed in BD Seven Bridges Genomics website. The multiplexing consisted of Tags assigned to each condition, as in metadata attached. For the target genes, Fastq files containing the raw sequencing were mapped against a reference panel (BD-Rhapsody_immune_Response_Panel_Hs.fasta). For whole transcriptome sequencing, Fastq files containing the raw sequencing were used to map against a reference genome (GRCh38-PhiX-gencodev29-20181205.tar.gz) with supplemental virus genome (Sars_cov_2.ASM985889v3.cds.all.fa), and transcriptome annotation (gencodev29-20181205.gtf)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 500"],"pubmed_abstract":["<h4>Introduction</h4>Factors regulating the severity of pneumonitis during viral infections remain unresolved. We previously found higher expression of protein S (PROS1) in lung epithelium of mild compared to severe coronavirus disease 2019 (COVID-19) patients. We hypothesized that PROS1 may protect the upper airways by regulating epithelial and myeloid cell responses during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection.<h4>Methods</h4>To test this, <i>in vitro</i> air-liquid interface (ALI) cultures of primary healthy human lung epithelial cells were infected with SARS-CoV-2. This model, validated through immunofluorescent staining, confocal microscopy, and single-cell RNA-sequencing, replicated pathogenic changes seen in the lungs of COVID-19. Regulation and secretion of PROS1, along with multiple soluble mediators, were quantified in control and infected cultures using ELISAs.<h4>Results</h4>We found that PROS1 is present in the basal cells of healthy pseudostratified epithelium and is released during SARS-CoV-2 infection through an IFN-mediated process. Transcriptome analysis revealed that PROS1 downregulated the SARS-CoV-2-induced proinflammatory phenotypes of basal cells, transforming pathogenic CXCL10/11<sup>high</sup> into a regenerative S100A2<sup>pos</sup>KRT<sup>high</sup> basal cell phenotype. In parallel, SARS-CoV-2 increased the secretion of M-CSF from epithelial cells, which induced the expression of PROS1 receptor MERTK on monocytes interacting with the lung epithelium. PROS1, in turn, shifted SARS-CoV-2-induced pathogenic monocyte phenotypes toward a phenotype with increased MHC class II.<h4>Conclusion</h4>These findings highlight the crucial role of PROS1 in protecting against severe lung pathology caused by SARS-CoV-2, by reducing epithelial- and monocyte-derived inflammation, promoting pro-repair epithelial phenotypes, and enhancing antigen presentation in myeloid cells."],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_title":["PROS1 released by lung basal cells limits inflammation in epithelial and monocytes during SARS-CoV-2 infection"],"pubmed_authors":["Theodoros Simakou","Simakou T, Szemiel AM, MacDonald L, Kerr K, Somma D, Diallo K, Frew J, Hardy OM, Doohan M, Elmesmari A, McSharry C, Alivernini S, Otto TD, Patel AH, Kurowska-Stolarska M."],"additional_accession":[]},"is_claimable":false,"name":"PROS1 released by lung basal cells limits inflammation in epithelial and monocytes during SARS-CoV-2 infection","description":"The data here represent two Single-Cell experiments performed to understand the roles of PROS1 in bronchial epithelial cells and monocytes, infected by SARS-CoV-2. The CVR EXP5 contains epithelial cultures grown on Air-Liquid Interface as mock or infected by the delta variant of SARS-CoV-2 (Delta B.1.617.2), and cocultures of mock or infected epithelium with CD14 monocytes. Some of these cultures were also supplemented with PROS1, to study the effects of the protein during infection. The CVR EXP1 contains cultures of PBMCs cultured in presence of SARS-CoV-2 variant (BetaCoV/England/02/2020/EPI_ISL_407073 ), with or without PROS1 supplementation. CVR EXP5 libraries were prepared using the Whole transcriptome Analysis and Sample Tag library Preparation kit (BD 633801), as per manufacture’s protocol (2019 version). CVR EXP1 libraries of 399 genes were prepared using BD Rhapsody Targeted mRNA and the Tag Amplification Kit (no. 633774) and primers from the BD Rhapsody Immune response Panel Hs (399 genes, BD 633750), as per manufacture’s protocol.","dates":{"release":"2025-10-17T00:00:00Z","modification":"2025-10-17T13:19:13.135Z","creation":"2024-09-03T10:32:12.752Z"},"accession":"E-MTAB-14405","cross_references":{"pubmed":["40980495"],"ENA":["ERP163737"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"],"doi":["10.1093/discim/kyaf012"]}}