Table 1 Current methods available for single-cell RNA sequencing
From: Single-cell sequencing technology applied to epigenetics for the study of tumor heterogeneity
Technique | Technical features | Designed by |
|---|---|---|
CEL-Seq | Lower throughput (hundreds to thousands of single cells); linear amplification sequencing method (lower cost); only be used for 3′ end sequencing; introduces barcode sequences; application to cellular heterogeneity and molecular mechanisms; suitable for exploring cellular heterogeneity and molecular mechanisms | [34] |
CEL-Seq2 | As an upgraded version of CEL-Seq1;introduces UMI (Unique Molecular Identifier) to eliminate sequencing bias introduced by PCR amplification | [35] |
MARS-Seq | High throughput (large numbers of single-cell samples); unique molecular tags enable hybrid sequencing of transcriptomes from multiple cells (lower cost); suitable for exploring heterogeneity in tumors and capturing spatial transcriptomic information | [36] |
MARS-Seq2 | As an upgraded version of MARS-Seq1;introduces UMI (Unique Molecular Identifier) to eliminate sequencing bias introduced by PCR amplification | [37] |
Quartz-Seq | High throughput (hundreds to thousands of individual cells); relatively high loss of cells during sample preparation; requires microfluidic chips; high cost; suitable for studying gene expression patterns and cellular heterogeneity in single cells | [38] |
Quartz-Seq2 | As an upgraded version of Quartz-Seq; highly sensitive and high throughput; technical noise and bias: amplification bias and loss of a portion of low abundance RNA; requires a certain number of cells to obtain sufficient RNA quality | [39] |
mcSCRB-seq | The mcSCRB-seq's "multi-channel" allows sequencing of multiple samples (reducing cost per sample), increasing throughput and efficiency; unique barcodes are incorporated during reverse transcription, allowing for the pooling and simultaneous sequencing of multiple cells | [40] |
Smart-Seq | Medium throughput (tens to hundreds of individual cells); high initial RNA volume requirements; bias and noise may be introduced during amplification; high cost per sample; captures full-length transcriptome information for detailed analysis of cell types or states with complex transcriptomic regulatory networks | [41] |
Smart-Seq2 | As an upgraded version of Smart-Seq; Introduction of UMI (Unique Molecular Identifier) sequences and sample-specific index sequences; Smart-Seq2 uses T7 RNA polymerase for amplification with higher amplification efficiency (VS Smart-Seq1 Linear amplification technique) | [42] |
Smart-seq3 | As an upgraded version of Smart-seq2, Smart-seq3 has 5′ UMI and achieves more efficient sequencing; Smart-seq3 is able to detect more genes, especially low abundance genes; Efficiently removes most of the ribosomal RNA (rRNA) | [43] |
ICELL8 | High throughput (thousands of cells on a single chip); unique microfluidic chip required; Multi-Hole Options; Sufficient number of cells is required to ensure good capture efficiency | [44] |
Drop-seq | Drop-seq is a microdroplet-based technology; high throughput (thousands of single cells can be processed and millions sequenced); Lower sample cost | [45] |
inDrop | Drop-seq is a microdroplet-based technology; high throughput (thousands of single cells can be processed and millions sequenced); Lower sample cost; inDrop introduces an indexing technique (compared to Drop-seq) that enables simultaneous sequencing of multiple samples through the introduction of barcoded beads; suitable for exploring cellular heterogeneity | [46] |