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. 2020 Aug 19;3:453. doi: 10.1038/s42003-020-01181-z

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© The Author(s) 2020

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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Fig. 3 — a Alternative splicing analysis with rMATS determined the abundance of skipped exon events in non-stem cell types compared to stem cells. b Breakdown of average percentages of rMATS splicing changes (events) detected between stem and all non-stem cell types by type of event (SE = skipped exon, RI = retained intron, MXE = mutually exclusive exon, A5SS = Alt 5 splice site, A3SS = Alt 3 splice site) showing predominance of SE (73%) (FDR < 0.05). c Crypt diagram illustrating cell types in the secretory lineage (SecPDG, tuft, EEC) versus absorptive lineage (AbsPro, Ent). A numeric SAR (splicing abundance ratio = number of significant alternative splicing changes ÷ number of significant gene expression changes x 100) arc indicates the number of splicing changes relative to gene expression between stem, progenitors, and differentiated cells. d Alternative polyadenylation (APA) analysis with DaPars quantitated the number of APA changes (events) in non-stem cells compared with stem. e APA events characterized by which cell type has the longer 3’UTR isoform for each polyadenylated mRNA in stem versus AbsPro (top) and stem versus SecPDG (bottom) (padj < 0.05). f Crypt diagram illustrating PAR (polyadenylation abundance ratio = number of significant alternative polyadenylation changes ÷ number of significant gene expression changes × 100) comparing polyadenylation changes to gene expression between stem, progenitors, and differentiated cells. Splicing and polyadenylation analysis was performed with the following biological replicate number of mRNA-seq samples: stem = 3, AbsPro = 3, SecPDG = 4, tuft = 5, Ent = 5, and EEC = 2.