Fig. 1
Schematic overview of experimental design. Graphics depict the esophagus, stomach, and the GE-SCJ tissue regions from mice at distinct developmental stages, including gestational days 15 and 19, newborn (2 days old), and adult (8 weeks old). Further, esophagus and stomach organoids were derived from adult epithelial stem cells to validate and complement physiological relevance. (i). single-cell preparation and capture: The initial step involves tissue or organoid digestion to obtain single cells and subsequent multiplexing of samples using the CMO (cell multiplexing oligos) technique followed by single-cell capture and barcoding using the 10X Genomics Chromium controller. (ii). Library preparation and sequencing: High-quality libraries for 3′ scRNA-seq are prepared and subjected to sequencing. (iii). Data processing and analysis: Upon sequencing, reads are aligned to the reference genome, and samples are demultiplexed, yielding a gene-by-cell count matrix. This matrix is then utilized in the Seurat workflow, facilitating robust data integration and spatial evaluation to measure the consistency and reliability of observations across datasets.
