Additional file 1 of A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients

Additional file 1: Supplementary tables. Table S1. Liver serum markers for COVID-19 and control liver samples. Table S2. NanoString GeoMx Digital Spatial Profiling (DSP) Whole Transcriptome Atlas (WTA) SARS-CoV-2 additional probe set. S3-Markers. Table S3. Significant genes and pathways following the zonation gradient in the GeoMx DSP WTA data. Table S4. Differentially expressed genes and pathways for each region of interest in the GeoMx DSP WTA data. Table S5. Differential abundance results comparing COVID with Control livers using a Binomial generalized linear mixed model (GLMM). Table S6. Summary of viral loads using RT-PCR and subgenomic mRNA assay in donors L1-5 who expired due to COVID-19 (LOQ: limit of quantification). Table S7. Association between clinical covariates and donor viral enrichment score. The association tests (Spearman correlation, Kendall’s tau and Wilcoxon rank sum test) were conducted for all samples from all medical centers (All. statistics, All. pvalue) as well as for the samples from medical center A separately (CentrerA.statistic, CenterA.pvalue). Table S8. Summary of liver histopathology findings for samples L1 to L4. H&E staining, CK19, and α-SMA IHC, as well as connective tissue staining (picrosirius red) were performed in four consecutive core biopsies samples and evaluated by an expert clinical liver pathologist (I.N.). Table S9. Curated pathway annotations and signatures used to estimate pathway activity scores.