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. 2019 Mar 14;9:4536. doi: 10.1038/s41598-019-40809-x

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Analysis of gastric organoid populations with immunofluorescence and single cell RNA-Seq. (a) H&E staining shows that the Trp53−/− organoid, cultured for three months, consist a layer of tall columnar epithelial cells with an outer lining of spindle-shaped fibroblastic stroma cells. (b) The IF showed that E-cadherin (E-cad) is expressed in epithelial cell layer (green) and Vimentin (Vim) is expressed in surrounding fibroblast cells (red). Nuclei are counterstained with DAPI (blue). (c) Overview of dissecting cell population using single cell RNA sequencing (scRNA-Seq). Individual cells were encapsulated with single gel beads coated with oligonucleotides in droplet partitions via a high throughput microfluidic device. mRNAs were reverse transcribed by the barcoded oligonucleotides in individual droplets. Subsequently, the droplets were broken and barcoded cDNAs were pooled together for PCR amplification to generate complete scRNA-Seq libraries for sequencing. BC - Barcode, UMI - Unique Molecular Identifier, SI - Sample Index.