Fig. 2: Application of scCHyMErA-Seq for the targeted deletion of 224 alternative cassette exons. | Nature Communications

Fig. 2: Application of scCHyMErA-Seq for the targeted deletion of 224 alternative cassette exons.

From: Single-cell exon deletion profiling reveals splicing events that shape gene expression and cell state dynamics

Fig. 2: Application of scCHyMErA-Seq for the targeted deletion of 224 alternative cassette exons.

a Schematic representation of the lentiviral scCHyMErA-Seq library targeting 224 alternative cassette exons for deletion and 161 genes for knockout. Blue and orange triangles indicate Cas9 and Cas12a target sites, respectively, for each hgRNA category. b Overview of the scCHyMErA-Seq experimental pipeline. Graphical elements were created in BioRender. c, d UMAP visualization of HAP1 cells expressing hgRNAs inducing gene-level knockouts (c) or exon deletions (d) following linear discriminant analysis (LDA). Insets show UMAPs recalculated after removal of cells associated with the highlighted perturbations in the original plots. Distinct clusters are labeled by the targeted gene or exon. Black dots denote cells carrying hgRNAs targeting other genes, exons, or intergenic controls.

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