What are the different types of single-cell sequencing?

Single-cell sequencing is a technology that measures various types of genetic material such as the transcriptome, genome, or methylome of a single cell. There are three types of single-cell sequencing. They differ primarily in terms of sample preparation and applications. 

Single-cell genome sequencing (scDNA-seq)

Single-cell genome sequencing analyzes the genome of single cells, revealing the genomic diversity within a cellular population. 

Sample preparation for single-cell genome sequencing involves isolating cells and amplifying their DNA using methods such as multiple annealing and looping-based amplification cycles (MALBAC) or multiple displacement amplification (MDA). MALBAC provides reduced but even genome coverage while MDA provides superior but uneven genome coverage. 

Single-cell genome sequencing is particularly useful in microbiome and cancer research. Using scDNA-seq, researchers can measure the genomes of the microbial components within microbiomes without isolating and cultivating them first. In cancer research, researchers can identify novel carcinogenic mutations and study intra-tumor genetic diversity using scDNA-seq. 

Single-cell transcriptome sequencing (scRNA-seq)

Single-cell transcriptome sequencing quantifies the RNA molecules in each cell of a given sample, providing insights into gene expression at the time of cell harvest. The procedure is also known as single-cell RNA sequencing or single-cell RNA-seq.

To prepare samples for single-cell transcriptome, cells are lysed, and mRNA is converted to complementary DNA (cDNA), which is then amplified. 

scRNA-seq has a wide range of applications. This technique is used to identify cell subpopulations, such as the malignant cells within a tumor mass and to study key gene transcription characteristics such as monoallelic gene transcription and splicing patterns. 

Single-cell DNA methylome sequencing (scDNA-Met-seq)

Single-cell DNA methylome sequencing focuses on DNA methylation patterns, an epigenetic mechanism that affects gene activity without altering its sequence. The process involves the transfer of a methyl group onto a cytosine carbon (often C5).

To prepare the sample for scDNA-Met-seq, DNA is treated with bisulfite to convert non-methylated cytosines to uracil before amplification. 

This technique is mainly used in developmental studies and cancer research to explore epigenetic changes within genetically identical cellular populations. scDNA-Met-seq is also used to study rare and highly active subpopulations of tumor cells.