Fresh, whole, and nontransplantable organs, or 1- to 2-cm3 organ samples, were obtained from surgery and then transported on ice by courier to tissue expert laboratories, where they were immediately prepared for transcriptome sequencing. Single-cell suspensions were prepared for 10× Genomics 3′ V3.1 droplet-based sequencing and for FACS-sorted 384-well plate smart-seq2. Preparation began with dissection, digestion with enzymes, and physical manipulation; tissue-specific details are available in the complete materials and methods (12 ). Cell suspensions from some organs were normalized by major cell compartment (epithelial, endothelial, immune, and stromal) using antibody-labeled magnetic microbeads to enrich rare cell types. cDNA and sequencing libraries were prepared and run on the Illumina NovaSeq 6000 with the goal to obtain 10,000 droplet-based cells and 1000 plate-based cells for each organ. Sequences were demultiplexed and aligned to the GRCh38 reference genome. Gene count tables were generated with CellRanger (droplet samples) or STAR and HTSEQ (plate samples). Cells with low unique molecular identifier (UMI) counts or low gene counts were removed. Droplet cells were filtered to remove barcode-hopping events and filtered for ambient RNA using DecontX. Sequencing batches were harmonized using scVI and projected to two-dimensional (2D) space with UMAP for analysis by the tissue experts. Expert annotation was made through the cellxgene browser and regularized with a public cell ontology. Annotation was manually QC checked and cross-validated with PopV, an annotation tool that uses seven different automated annotation methods. For complete materials and methods, see the supplementary materials (12 ).