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. 2021 Dec 6;22:331. doi: 10.1186/s13059-021-02554-1

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© The Author(s) 2021

Open AccessThis 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/. 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 in a credit line to the data.

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Fig. 1 — a Overview of single-cell short/long-read integration strategy of RACK1 targeting. b Structure of RACK1 transcript. c, d Two heatmaps showing the proportion of each transcript isoform (x-axis) with each cell (y-axis) for either the single (c) or multiplexed (d) CRISPR edits respectively. For panel c, hierarchical clustering was conducted on the cells subject to a single CRISPR edit of exon 5. Cluster 2 has the intact RACK1 isoform with all exons. Cluster 1 cells demonstrate exon 5 skipping. For panel d, hierarchical clustering was conducted on cells subject to multiplexed edits across different exons. Cluster 3 indicates the cells with an intact RACK1 transcript. The remaining clusters demonstrate cells with exon skipping. e Expression level of RACK1 in each cell cluster denoted in panel d. P values were calculated for each cluster in comparison with Cluster 3 (C1 P = 5.7e−12, C2 2.6e−11, C4 9.9e−11, C5 1.6e−10, C6 1.1e−07, C7 9.5e−06, C8 2.5e−07, C9 1.1e−08 ; two-sided t-test)