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. 2018 Sep 25;9:3903. doi: 10.1038/s41467-018-06423-7

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© The Author(s) 2018

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. 4 — Location-dependent features are imprinted within selected SC subsets. Single cell suspensions from mLNs and pLNs were sorted for CD24⁻CD45⁻ cells and subjected to scRNA-seq. Non-endothelial SCs were identified as non-LECs, non-BECs, and Pecam1⁻ and Ackr4⁻. Data pooled from two independent experiments. a t-SNE plot of merged pLN SCs and mLN SCs showing cluster segregation. b Expression of subset-defining DEGs across all non-endothelial SCs on t-SNE plot. c Heatmap of 272 DEGs (up to 20 per cluster) with the most significant differential expression (minimal FDR-adjusted p-value). Marker genes for respective clusters are indicated with arrows. d Heatmap (left) depicts average expression per cluster of genes persistently up-regulated in SCs from transplanted mLN-SPF. Bargraph (right) shows cumulative Z-score (cZscore) of average expression per cluster for the genes persistently up-regulated in SCs from transplanted mLN-SPF. e Expression of indicated genes persistently up-regulated in non-endothelial SCs from transplanted mLN-SPF on t-SNE plot for mLN-SPF and pLN-SPF scRNA-seq. BEC blood endothelial cell, DEG differentially expressed gene, mSC metabolic stromal cells, pSC proliferating stromal cells, PvC perivascular cells, SC stromal cell, LEC lymphatic endothelial cell, t-SNE t-distributed stochastic neighbor embedding