{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Olivier Terrier"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16265"],"description":["Respiratory viral coinfections pose a substantial global health burden, yet the underlying virus–virus interactions remain incompletely understood. Here, we systematically examined the interplay among influenza A virus (IAV), SARS-CoV-2, and respiratory syncytial virus (RSV) using a reconstituted human airway epithelium model. We monitored viral replication dynamics and host transcriptional responses under both simultaneous and sequential infection conditions."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - The SARS-CoV-2 strain used in this study was isolated from a patient enrolled in a French clinical cohort of COVID-19 patients (ClinicalTrials.gov identifier NCT04262921; The sequence is available in the GISAID EpiCoV™ database under the accession BetaCoV/France/IDF0571/2020 (EPI_ISL_411218). Viral stocks were amplified and titrated by determination of the 50% tissue culture infectious dose (TCID₅₀/mL) on Vero cells (ATCC CRL-1586). The influenza A/Lyon/969/2009 (H1N1) strain was propagated and titrated on MDCK cells (ATCC CCL-34). A recombinant RSV A2 strain expressing mCherry (RSV-mCherry, kindly provided by Jean-François Eléouët, INRAE, Jouy-en-Josas, France) was propagated and quantified on LLC-MK2 cells (ATCC CCL-7). For infection, HAE were gently washed twice at the apical surface with Opti-MEM (Life Technologies) and subsequently mock-infected (Opti-MEM) or infected with SARS-CoV-2, IAV, or RSV at multiplicities of infection (MOI) of 0.01, 0.1, and 0.2, respectively. At defined time points, apical washes and basal media were collected and stored at −80°C for further analyses. Cells were lysed for total RNA extraction, which was used for RT-qPCR and RNA-seq. All experiments involving infectious SARS-CoV-2 material were performed in a biosafety level 3 (BSL-3) facility, while infections involving only IAV and/or RSV were conducted in a biosafety level 2 (BSL-2) laboratory.","Nucleic Acid Extraction - Briefly, HAE were lysed in RLT buffer (Qiagen RNeasy® Plus Mini Kit, ref. 74136) and scraped before collection. Total RNA was extracted using the same kit according to the manufacturer’s instructions.","Sequencing - Final samples pooled library prep were sequenced on an ILLUMINA NextSeq 2000 with a P2-100 cycles cartridge (1*400 million 100-base reads), corresponding to 1*13 million reads per sample after demultiplexing.","Library Construction - RNA library preparation was realized following the manufacturer’s recommendations (QuantSeq 3’ mRNA-Seq V2 Library Prep Kit from LEXOGEN)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw counts were normalized to log10-Counts Per Million (logCPM) by dividing each column by the total sum of its counts, multiplying it by 106, followed by the application of a log10-transform."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_title":["Dynamics of interactions between three major respiratory pathogens in reconstituted human epithelium"],"pubmed_authors":["Aurélien Gibeaud, Charles Terra, Émilie Portier,  Pascal Lukas, Audrey Le Gouellec, Jeremie Guedj, Frederik Graw, Andrés Pizzorno, Olivier Terrier","Olivier Terrier"],"additional_accession":[]},"is_claimable":false,"name":"Dynamics of interactions between three major respiratory pathogens in reconstituted human epithelium","description":"Respiratory viral coinfections pose a substantial global health burden, yet the underlying virus–virus interactions remain incompletely understood. Here, we systematically examined the interplay among influenza A virus (IAV), SARS-CoV-2, and respiratory syncytial virus (RSV) using a reconstituted human airway epithelium model. We monitored viral replication dynamics and host transcriptional responses under both simultaneous and sequential infection conditions.","dates":{"release":"2026-01-30T00:00:00Z","modification":"2026-01-31T02:02:07.334Z","creation":"2025-11-26T15:16:03.571Z"},"accession":"E-MTAB-16265","cross_references":{"ENA":["ERP185682"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}