library_construction_protocol: For the single-cell RNA sequencing experiments each organoid was generated from 4 different donors. After organoid dissociation into single-cell suspension using TrypLE express (ThermoFisher Scientific Cat#12604012), cells were counted, and pooled together (78,000 total cells). Pooled cells were then loaded evenly across two lanes in the Chromium Controller for generating single-cell contained in lipid droplets following the manufacturer's instructions (10X Genomics). A Chromium Single cell 3' Reagent Kit (v3.1) (10X Genomics) was used for reverse transcription, cDNA amplification and library construction of the gene expression libraries following the manufacturer's instructions. All samples were encapsulated, and cDNA was generated within 6 hours after organoid processing. MULTISeq barcode libraries were generated using the protocol describedin Mcginnis et.al, Nature Methods (2019). Finally, Pooled libraries were sequenced on an Illumina NovaSeq 6000. roose-1/2_GEX: 10X 3' Gene Expression; roose-1/2_MSQ: MULTI-Seq tagging of Single Cells using Lipid Barcodes