Table 1 Comparison of published single-cell RNAseq isoform studies
From: Single-cell RNAseq for the study of isoforms—how is that possible?
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] | 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 | |