Table 1.

Different types of single-cell sequencing methodologies applied in Hepatocellular carcinoma.

Steps/Technique	Smart-Seq2	CEL-Seq2	10×-Chromium	scATAC-Seq	TARGET-Seq
Cell isolation approach	Low throughput	High throughput	High throughput	High throughput	High throughput
Platform	96/384-well plates; Illumina HiSeq 2000	96/384-well plates; Fluidigm C1, illumine TrueSeq	Drop Seq: Cells with barcoded beads with unique molecule identifiers (UMIs) and primers are used	10× Genomics; Illumina NextSeq 500	Plate-based, Illumina NextSeq 500/550
Measurement	Transcriptome	Transcriptome	Transcriptome	Epigenomics	Genomics
Reverse transcription and c-DNA amplification	Polymerase chain reaction (PCR)	in vitro transcription (IVT). UMI and specific bar codes are used for easy pooling	PCR. UMI and specific bar codes are used for easy pooling	PCR; Barcoded primers	PCR; Barcoded RT primers
Library generation	Tagmentation	Fragmentation	Tagmentation and 3′ enrichment	Tagmentation	Tagmentation
Gene coverage	Full length	3′ part of the gene is sequenced	3′ part of the gene is sequenced	Full length	3′-biased and full length
Sensitivity	High (increasing sensitivity for the detection of low-abundance transcripts, reducing bias towards longer genes, and enabling additional analyses such as assessment of splice variants).	High	High (to quantify individual transcripts, reducing technical noise and amplification bias, but introducing 3′ or 5′ bias depending on the transcript end receiving the tag). Drop-seq exhibits lower capture efficiency and resolution.	Fast and sensitive epigenomic profiling; High variability analysis	High sensitivity, detects multiple mutations in a specific single cell, detects biallelic mutations, detect genomic DNA variants, targeted amplification
Cost	High	Slightly low	Low	High	High
Reference	[29]	[30]	[29]	[31]	[32,33]