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. 2023 May 12;14:2734. doi: 10.1038/s41467-023-38409-5

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© The Author(s) 2023

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 — a t-SNE analysis of nuclei isolated from FFPE mouse kidney sample by snRandom-seq based on their gene expressions and colored by identified cell types. Fourteen Cell types identified were colored and shown below. b Expression of selected three cell-type markers in single nuclei in the t-SNE maps of FFPE mouse kidney. Gene expression levels are indicated by shades of red. c Dot plot of the average expressions of top two markers in each of the 14 cell types. d Proportion of annotated cell types of FFPE1, FFPE2, and fresh samples by snRandom-seq. e t-SNE and RNA velocity analysis of snRNAs from FFPE mouse testis by snRandom-seq. Velocity is shown as black arrows in different cell types by separate colors. The black arrows indicate RNA maturation trajectory. f Percents of spliced and unspliced transcripts in different cell types. g Cell cycle analysis of FFPE mouse testis by snRandom-seq. Points in t-SNE were colored by identified cell cycle phases (G1, G2M, or S). Red dashed circle: two subpopulations of late spermatocytes at the G2M phase with active transcriptional activity. Source data are provided as a Source Data file.