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. 2023 Sep 25;42(8):1218–1223. doi: 10.1038/s41587-023-01948-9

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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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Extended Data Fig. 10 — a. UMAP embedding of cells with miRNA pathway genes knockdowns and NTC cells reflected the cell-cycle progression. b. Stacked barplot showing the cell cycle distribution of cells from each perturbation. c. The expression changes of cell cycle marker genes in cell cycle clusters. d. The cell cycle time-course synthesis rates, degradation rates, and steady-state expression changes of 4 gene clusters. Solid lines with dots, the mean values and the average trend of all genes within the cluster. e. The top enriched GO terms of genes in the cluster 1 identified in GO enrichment analysis. f. Averaged trends of cell cycle time-course synthesis rates, degradation rates, and steady-state expression changes of cluster 1 genes in HEK293-idCas9-sgNTC, sgDROSHA, sgDICER1 cells. g. Averaged trends of cell cycle time-course synthesis rates, degradation rates, and steady-state expression changes of genes in cluster 1 in HEK293-idCas9-sgNTC and sgLRPPRC cells. Considering potential strong batch effects from distinct genetic perturbation, cell cycle clustering analysis in (g) was performed independently of (a), and cell cycle clusters in (g) were not fully synchronized with clusters in (f).