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. 2020 Oct 22;10:18100. doi: 10.1038/s41598-020-75238-8

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© This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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Comparison of Ctrl, MethFix and RNAlater datasets. snRNASeq datasets. (a) Ctrl, (b) MethFix and (c) RNAlater, were clustered by modularity-based clustering method with Leiden optimization algorithm, and visualized by 2D UMAP embedding. (d) Increased number of genes detected per nucleus in sample preservation datasets (1682 median genes per nuclei in MethFix, 1857 median genes per nuclei in RNAlater) compared to Ctrl dataset (727 median genes per nuclei) (one-way ANOVA p < 0.0001), while no significant difference between MethFix and RNAlater dataset (post hoc t-test, p = 0.88). (e) Major SV cell types (marginal, intermediate, basal), spindle-root and Reissners’ membrane cells are detected in all three datasets, but other small populations of cells (fibrocyte,macrophage, RBC, B cell and neutrophil ) are detected in either Ctrl or MethFix/RNAlater datasets. Ctrl, MethFix and RNAlater datasets are integrated by Harmony and visualized by 2D UMAP embedding. Integrated cells are colored based on (f) cell identities or (g) original dataset (Ctrl, MethFix, RNAlater).