GSM5504177: RNA of scRNA-seq of 3 single rosette organoids at 3-month old each with HTO tag A, B or C; Homo sapiens; RNA-Seq
One-, three-, or five-month SOSRS were dissociated using the Worthington papain dissociation kit. Cells from each organoid were labelled with sample-specific hashtag-labelled antibodies (HTO-A, Biolegend) to allow multi-sample pooled analyses to reduce batch effects, with subsequent de-multiplexing of scRNA-seq data based on the hashtags. Single-cell suspensions were processed using the 10X Genomics Chromium platform, and scRNA-seq libraries were sequenced by Illumina NovaSeq. Each paired-end read contains a cell barcode and a UMI in Read 1, and the transcript-specific read in Read 2 with a read length of 151 nt.  Separately, each cell generates an HTO count vector for the hashtags used, allowing the cells to be assigned to organoid samples they come from.