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. 2019 May 9;20:90. doi: 10.1186/s13059-019-1699-y

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© The Author(s). 2019

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 3 — CellTag Indexing revealed iEP engraftment and transition through an intestinal stem cell fate. a CellTags identified engrafted iEPs enriched in cluster 4 (early engraftment iEPs) and the main intestinal epithelial clusters. b Density heatmap confirms enrichment of CellTagged cells in the early engraftment iEP cluster and the main intestinal epithelial cell clusters. c, d Stacked bar plots of CellTagged cells show enrichment in clusters 0, 1, and 4. e Permutation test of cluster enrichment or depletion for each CellTag in intestinal clusters show statistically significant enrichment of Ecad^High/CellTagA cells in cluster 0 (Lgr5⁻ Lrig1⁺ ISCs, p = 4.03 × 10^− 5) and cluster 1 (Lgr5⁺ ISCs, p = 9.83 × 10^− 3). y-axis, negative log10 of p value for cluster enrichment, log10 of p value for cluster depletion. Dotted lines correspond to a p value of 0.05. f RNA velocity analysis shows velocity vectors from iEPs towards Lgr5⁻ Lrig1⁺ ISCs and from the ISC clusters towards the differentiated enterocyte clusters. g Subset of velocity vectors of CellTagged cells confirm transcriptional kinetics of engrafted iEPs in the direction towards intestinal stem cells