Fig. 6: Proteome analysis of SARS-CoV-2-infected JFB organoids at 48 h.

JFB distal SI organoids (bat003, p9) were infected with SARS-CoV-2 at an MOI of 10 or underwent mock treatment for 48 h and then were lysed and processed for data-independent acquisition (DIA) mass spectrometry. N = 3 replicates from one organoid line were analyzed. lmfit with empirical Bayes smoothing, a linear regression model from the Limma R package, was used with FDR correction for multiple tests. a Volcano plot showing all detected proteins and protein isoforms. Proteins with significantly increased or decreased expression ( ≥ 2-fold change; P ≤ 0.05) are shown in red and blue. b Expression of interferon-stimulated genes (ISGs), identified based on OhAinle et al. (2018)⁶⁵, in mock-infected and SARS-CoV-2 infected JFB organoids. Proteins with significantly increased or decreased expression ( ≥ 2-fold change; P ≤ 0.05) are shown in red and blue. c Heatmap showing relative change (Z-scores) of all 27 significantly upregulated proteins and of the top 30 downregulated proteins (P ≤ 0.05). Data from triplicate cultures are shown. Protein function was determined using UniProtKB (H. sapiens). Significantly regulated ISGs are highlighted in yellow. d IPA analysis showing top regulated canonical signaling pathways (top) and molecular and cellular functions (bottom) activated in SARS-CoV-2 infected JFB organoids. Enrichr pathway analysis using (e) the 2021 human KEGG pathway database and (f) the 2021 COVID-19 related gene sets. Pathways were ranked based on combined score ranking. Source data are provided via the PRIDE partner repository with the dataset identifier PXD036016.