Extended Data Fig. 1: Immunohistochemistry and snRNAseq library quality metrics.
a) Images of Hematoxylin eosin- (HE), CD3-, and CD68-stained and b) of CD4- and CD8- stained EMB sections. Representative images from each group are shown. Stainings on EMB sections were performed for all patients (Non-COVID-19: n = 8, Post-COVID-19: n = 10, Post-Vaccination: n = 4, MISC: n = 2). Cell counts are presented in Extended Data Table 1. c) Size of human left ventricular endomyocardial cardiac biopsies (EMBs) for snRNA-seq. The image shows different EMB tissue sizes and their weight before nuclei isolation in a 5 cm dish on ice. d) Violin plots showing number of detected genes (n_genes), detected UMIs (n_counts), fraction of UMIs mapping to mitochondrial-encoded genes and ribosomal genes and doublet probabilities according to scrublet and solo per nucleus within a cell-type. Distributions have been computed for all samples and subsetted for explants and EMB samples only. e) Barcode rank plots across all EMB (n = 25) and explant samples (controls n = 18). Clear distinction between nuclei containing droplets and empty droplets (background ambient RNA) indicated a low overall background. f) Box plots showing snRNA-seq library quality metrics. Boxes depict the interquartile range (IQR), horizontal bars represent the median, whiskers extend to 1.5 × IQR. Data points outside the whiskers show measurements beyond Q1 or Q3 ± 1.5* IQR. Estimated numbers of nuclei pre-QC filtering, mean reads per nucleus in the fastq files, median UMI counts per cell and the cDNA concentration per sample were depicted between EMB (Non-COVID-19, Post-COVID-19, Post-Vaccination, PIMS; n = 25) and explant tissue material (controls n = 18).
