Table 1.

Comparison of published single-cell RNAseq isoform studies

		Reference	Main focus of the study	Full-length isoforms?	Computatio-nal method	Aim	Organism, cell type	Library prep	Feature or event targeted
Illumina sequencing		Ramskold et al. [39]	Single-cell RNAseq, genes	✗	MISO Developed for bulk RNAseq	Experimental protocol development Library preparation	Human, cancer cells	Smart-seq	Exon inclusion quantification
		Shalek et al. [36]	Single-cell RNAseq, genes and isoforms	✗	MISO Developed for bulk RNAseq	Single-cell heterogeneity in immune response	Mouse, BMDCs	Smart-seq	Exon inclusion quantification
		Zhang et al. [40] Data from Shalek et al. [36]	Bulk RNA-seq, isoforms	✗	WemIQ Developed for bulk RNAseq + single-cell validation	Computational method development Isoform identification	Mouse, BMCDs	Smart-seq	Single-cell bias in differential isoform detection
		Marinov et al. [35]	Single-cell RNAseq, genes and isoforms	✗	Pervouchine et al. [48] Developed for bulk RNAseq	Single-cell isoform and gene expression heterogeneity	Mouse, lymphobl-astoid cells	Smart-seq	Novel splice junctions, exon inclusion quantification
		Velten et al. [44]	Single-cell RNAseq, isoforms	✗	BATBayes	3′ UTR variability among genes and cells	Mouse, ESCs	BATSeq	Alternative poly(A) sites
		Welch et al. [42] Data from Buettner et al. [17]	Single-cell RNAseq, isoforms	✗	SingleSplice	Computational method development Differential isoform usage	Mouse, ESCs	Smart-seq/C1	Differential isoform usage
		Karlsson et al. [45] Data from Zeisel et al. [18]	Single-cell RNAseq, isoforms	✗	Alignment to FANTOM 5 database Developed for CAGE	Single-cell isoform expression heterogeneity	Mouse, brain cells	STRT-seq/C1	Alternative TSS
		Song et al. [38]	Single-cell RNAseq, isoforms	✗	Expedition	Computational method development Differential exon inclusion/exclusion	Human, iPSCs, NPCs and MNs	Smart-seq/C1	Exon inclusion quantification
		Huang et al. [43] Data from Wu et al. [49] and Scialdone et al. [50]	Single-cell RNAseq, isoforms	✗	BRIE	Computational method development Differential exon inclusion/exclusion	Human HCT116 cells + mESCs	Smart-seq + Smart-seq2	Exon inclusion quantification
Single-molecule sequencing	Oxford Nanopore	Byrne et al. [46]	Single-cell RNAseq, isoforms	✓	Mandalorion	Computational method development Isoform structure and quantification	Mouse, B1 cells	Smart-seq2	TSS, TTS, exon inclusion, intron retention, alt. 3′ and 5′ splice sites
	PacBio	Karlsson and Linnarsson [47]	Single-cell RNAseq, isoforms	✓	Self-designed pipeline	Single-cell isoform expression heterogeneity	Mouse, oligoden-drocytes and VLMCs	STRT-seq/C1	TSS, TTS, exon inclusion, alt. 3′ and 5′ splice sites

Illumina involves short-read sequencing, and single-molecule sequencing involves long-read technologies. Studies are classified per ‘focus’, either bulk-RNAseq, single-cell RNAseq for gene expression or isoform single-cell RNAseq (or both). Only ‘computational methods’ used for isoform identification/quantification are specified. ‘Full-length’ is only considered as such when isoforms were reconstructed end-to-end, regardless of whether library preparation was full-length or not. Text in italics adds complementary information on the aim of the computational method/library protocol developed. When specified, the study was performed on data generated by other authors. ‘Feature/event targets’ refer to the approach taken to study isoform diversity, or to a specific aspect of it that is tackled. For more information, readers should refer to this review’s analysis or to the referenced papers

BMDC bone-marrow-derived dendritic cell, ESC embryonic stem cell, iPSC induced pluripotent stem cell, mESC murine embryonic stem cell, MN motor neuron, NPC neural progenitor cell, TSS transcription start site, TTS transcription termination site, UTR untranslated region, VLMC vascular and leptomeningeal cell