{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Valeria Fernandez Vallone"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15980"],"description":["hiPSC from 2 different donors were differentiated into alveolar-like organoids (iPSC-aLOs) as previously described (DOI: 10.1038/s41596-019-0220-0). iPSC-aLOs were either kept in \\\"dome\\\" culture embedded in extracellular matrix or inverted in apical-out conformation to allow influenza H3N2 infection. Apical-out iPSC-aLOs were exposed or not to H3N2. At 24hs post-infection iPSC-aLOs were collected and dissociated into single cells. Samples were multiplexed using membrane lipid barcoding and we followed 10X Genomics instructions from single cell encapsulation to NGS. This data set is useful to compare iPSC-aLOs cell composition both in dome and apical-out culture conditions and iPSC-aLOs response to influenza virus H3N2 infection at a single timepoint of 24hs post-infection at MOI =1. Each sample (HUB 07-09) contains multiplexed conditions: control in dome culture, control in apical out (both non infected), infected 24 hpi. Due to human data sensitivity concerns, this experiment was submitted with processed data only."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - iPSC-aLOs still embedded in ECM were removed from the dome using a solution of collagenase/Dispase. After washing with PBS organoids were dissociated in single cells using Trypsin 0.25% / EDTA 2mM in PBS.","Library Construction - Nucleic acid library construction was performed following protocol CG000315 Rev F from 10X Genomics","Growth Protocol - iPSC-aLOs differentiation and culture was done as described in Jacobs et al. doi.org/10.1038/s41596-019-0220-0","Nucleic Acid Extraction - Nucleic acid extraction was not performed in this experiment. Each cell encapsulated was lysed within the oil droplet.","Sequencing - Nucleic acid sequencing was performed following protocol CG000315 Rev F from 10X Genomics","Sample Treatment - H2N3 was incubated with MOI=1 for 1h at 37°C. After washing samples were incubated for 24hs (endpoint as hour post infection)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - No normalization data transformation protocol was applied in this experimental set up"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"pubmed_abstract":["Immunocompromised patients, such as those undergoing hematopoietic stem cell or solid organ transplantation, are highly susceptible to viral complications. Given the limitations and side effects of available antiviral therapies, adoptive transfer of antiviral T cells offers a promising alternative by restoring immune defense. However, existing models for evaluating antiviral T cell therapies lack physiological relevance, limiting accurate predictions of efficacy and safety. There is a critical need for  in vitro human infection platforms that support personalized assessment of therapeutic responses. To address this, we developed antiviral T cell products (TCPs) targeting Influenza A virus (IAV)-infected cells, alongside an autologous human induced pluripotent stem cell (iPSC)-derived 3D lung organoid infection platform. This model recapitulates key immunological responses and is compatible with a new 3D high-throughput, high-content imaging pipeline. Our study provides the first proof-of-concept for assessing T cell-mediated cytotoxicity in a 3D  in vitro lung infection model, advancing personalized antiviral immunotherapy development."],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_title":["An autologous human iPSC-derived 3D organoid infection model for preclinical testing of antiviral T cells"],"pubmed_authors":["Valeria Fernandez Vallone","Ugarit Daher, Valeria Fernandez-Vallone, Morris Baumgardt, Benedikt Obermayer, Niklas Wiese, Achim Klaus Kirsch, Tanja Fisch, Anna Löwa, Michael Schmueck-Henneresse, Andreas C. Hocke, Leila Amini, Harald Stachelscheid"],"additional_accession":[]},"is_claimable":false,"name":"Single-cell RNAseq of hiPSC derived alveolar-like lung organoids upon H3N2 infection","description":"hiPSC from 2 different donors were differentiated into alveolar-like organoids (iPSC-aLOs) as previously described (DOI: 10.1038/s41596-019-0220-0). iPSC-aLOs were either kept in \\\"dome\\\" culture embedded in extracellular matrix or inverted in apical-out conformation to allow influenza H3N2 infection. Apical-out iPSC-aLOs were exposed or not to H3N2. At 24hs post-infection iPSC-aLOs were collected and dissociated into single cells. Samples were multiplexed using membrane lipid barcoding and we followed 10X Genomics instructions from single cell encapsulation to NGS. This data set is useful to compare iPSC-aLOs cell composition both in dome and apical-out culture conditions and iPSC-aLOs response to influenza virus H3N2 infection at a single timepoint of 24hs post-infection at MOI =1. Each sample (HUB 07-09) contains multiplexed conditions: control in dome culture, control in apical out (both non infected), infected 24 hpi. Due to human data sensitivity concerns, this experiment was submitted with processed data only.","dates":{"release":"2025-11-27T00:00:00Z","modification":"2026-05-27T15:02:23.55Z","creation":"2025-11-13T14:31:10.591Z"},"accession":"E-MTAB-15980","cross_references":{"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"],"doi":["10.1101/2025.09.16.676521"]}}