Human bronchial lung organoids
Single cell data were generated using the BD Rhapsody system implementing the Single-Cell Capture and cDNA Synthesis with BD Rhapsody Single-Cell Analysis System Protocol (Doc ID: 23-22951(02)) and the BD Rhapsody System mRNA Whole Transcriptome Analysis (WTA) and Sample Tag Library Preparation Protocol (Doc ID: 23-24119(03)). Samples were individually hash-tagged with the BD Flex Single-Cell Multiplexing Kits (Cat. No. 633849-633852) and the respective protocol [Doc ID: 23-24311(01)], combined with a PE-labelled primary antibody against ß2-microglobulin (Cat. No. 551337; all reagents from BD Biosciences, Heidelberg, Germany) at a 1:5 dilution. The libraries of ~11,000 captured cells were sequenced on an Illumina Novaseq6000 Sequencer with 57,000 reads/cell at the Genomics and Bioinformatics Platform of the Institute of Lung Health, University Giessen, Germany. Raw data were processed using the standard settings on the BD Rhapsody Sequence Analysis Pipeline (Revision: 0) at sevenbridges.com. Processed data was filtered based on the following criteria: mitochondrial percentage <40%, nCount >300, nFeatures between 300 and 10,000 and log10GenesPerUMI > 0.8. One sample was found to dominate the analysis; therefore, it was randomly downsampled to 450 cells, resulting in a total of approximately 7,000 high-quality cells for further analysis.
Single cell data were generated using the BD Rhapsody system implementing the Single-Cell Capture and cDNA Synthesis with BD Rhapsody Single-Cell Analysis System Protocol (Doc ID: 23-22951(02)) and the BD Rhapsody System mRNA Whole Transcriptome Analysis (WTA) and Sample Tag Library Preparation Protocol (Doc ID: 23-24119(03)). Samples were individually hash-tagged with the BD Flex Single-Cell Multiplexing Kits (Cat. No. 633849-633852) and the respective protocol [Doc ID: 23-24311(01)], combined with a PE-labelled primary antibody against ß2-microglobulin (Cat. No. 551337; all reagents from BD Biosciences, Heidelberg, Germany) at a 1:5 dilution. The libraries of ~11,000 captured cells were sequenced on an Illumina Novaseq6000 Sequencer with 57,000 reads/cell at the Genomics and Bioinformatics Platform of the Institute of Lung Health, University Giessen, Germany. Raw data were processed using the standard settings on the BD Rhapsody Sequence Analysis Pipeline (Revision: 0) at sevenbridges.com. Processed data was filtered based on the following criteria: mitochondrial percentage <40%, nCount >300, nFeatures between 300 and 10,000 and log10GenesPerUMI > 0.8. One sample was found to dominate the analysis; therefore, it was randomly downsampled to 450 cells, resulting in a total of approximately 7,000 high-quality cells for further analysis.
Kim Pauck