Single-Cell Exon Deletion Profiling Reveals Splicing Events That Shape Gene Expression and Cell State Dynamics

Kumari B, Damodaran AP, Guiblet WM, Xiao M, Behera AK, On TA, McIntosh CE, Teszler M, Holloway C, Le S, Parab N, Zhao Y, Aregger M, Gonatopoulos-Pournatzis T
Nat Commun 17, 1218 (2026) Article

Plasmids from Article

ID	Plasmid	Purpose
237451	pLCHKOv4	Lentiviral backbone for expressing U6-driven hybrid guide (hg)RNAs for scCHyMErA-Seq experiments.
237452	pLCHKOv5	Lentiviral backbone for expressing doxycycline (Dox)-inducible, Pol II-driven hybrid guide (hg)RNAs.
237453	pcDNA5-miniTurbo-NRF1-FL	Vector for generating Flp-In cell lines allowing dox-inducible mammalian expression of miniTurbo fused to full-length NRF1 isoform
237454	pcDNA5-miniTurbo-NRF1-∆ex7	Vector for generating Flp-In cell lines allowing dox-inducible mammalian expression of miniTurbo fused to NRF1 isoform lacking the alternative exon-7 (∆ex7)
237455	pcDNA5-3xFLAG-NRF1-FL_WobbleMut	Vector for generating Flp-In cell lines allowing dox-inducible mammalian expression of 3xFlag-tagged full-length NRF1 isoform mutated to be resistant to NRF1 siRNA
237456	pcDNA5-3xFLAG-NRF1-∆ex7_WobbleMut	Vector for generating Flp-In cell lines allowing dox-inducible mammalian expression of 3xFlag-tagged NRF1 isoform lacking the alternative exon-7 (∆ex7) mutated to be resistant to NRF1 siRNA
237457	pCS2+ Flag	Vector for constitutive mammalian expression of gene of interest
237458	pCS2+ Flag-SRSF3_WobbleMut	Vector for constitutive mammalian expression of Flag-tagged full-length SRSF3 mutated to be resistant to SRSF3 siRNA
237459	pET01-NRF1-Ex7-minigene	Vector for constitutive expression of NRF1 alternative exon-7 minigene
237460	pX461-ABE8e-nSpCas9	Transfection-based all-in-one base editor plasmid that expresses both adenine base editor (ABE8e-nSpCas9) and single guide RNAs (sgRNA) with BpiI cloning sites to clone sgRNA.
237461	pX461-evoCDA1-nSpCas9	Transfection-based all-in-one base editor plasmid that expresses both cytosine base editor (evoCDA1-nSpCas9) and single guide RNAs (sgRNA) with BpiI cloning sites to clone sgRNA.
237462	pX462-ABE8e-nSaCas9	Transfection-based all-in-one base editor plasmid that expresses both adenine base editor (ABE8e-nSaCas9) and single guide RNAs (sgRNA) with BpiI cloning sites to clone sgRNA.
237463	pX461-ABE8e-nSpCas9-Intergenic sgRNA	All-in-one base editor expressing adenine base editor (ABE8e-nSpCas9) and gRNA control targeting Intergenic site
237464	pX461-evoCDA1-nSpCas9-Intergenic sgRNA	All-in-one base editor expressing cytosine base editor (evoCDA1-nSpCas9) and sgRNA control targeting Intergenic site
237465	pX462-ABE8e-nSaCas9-Intergenic sgRNA	All-in-one base editor expressing adenine base editor (ABE8e-nSaCas9) and sgRNA control targeting Intergenic site
237466	pX461-ABE8e-nSpCas9-NRF1-ss-sgRNA	All-in-one adenine base editor (ABE8e-nSpCas9) with gRNA targeting NRF1-Ex7 splice site
237467	pX461-evoCDA1-nSpCas9-NRF1-ss-sgRNA	All-in-one cytosine base editor (evoCDA1-nSpCas9) with sgRNA targeting NRF1-Ex7 splice site
237468	pX462-ABE8e-nSaCas9-NRF1-ss-sgRNA	All-in-one adenine base editor (ABE8e-nSaCas9) with gRNA targeting NRF1-Ex7 splice site
237473	scCHyMErA-Seq Exon Deletion Library 1	Enables high-throughput identification of frame-preserving exons that influence transcriptional phenotypes, building on the CHyMErA system (Nature Biotechnology, 2020; PMID: 32249828).
237553	Topo_SpCas9.tracrRNA-CS1_AsCas12a DRv10	TOPO vector for the cloning of the SpCas9 tracrRNA-CS1 - AsCas12a Direct Repeat (DR) v10 fragment into the pLCHKO_v4 hgRNA vector for scCHyMErA-Seq experiments.