Fig. 1

Overview of current common SCS approaches and analyses. 1. scRNA-seq: By capturing transcripts and generating sequencing libraries for individual cells, scRNA-seq assesses biological properties of cell populations at unprecedented resolution. Several platforms are available, including Drop-seq, Smart-seq2, MARS-seq, and 10X Genomics. 2. scDNA-seq & methylation: Also known as single-cell genomic sequencing, whole genomic DNA from individual cells is captured, amplified, and sequenced. scDNA-seq can provide information on copy numbers and single nucleotide variants (SNVs). 3. scATAC-seq: A single-cell assay for transposase-accessible chromatin sequencing, provides a way to understand the regulatory landscape of the genome. 4. scCHIP-seq: Single-cell chromatin immunoprecipitation sequencing reveals the epigenetic heterogeneity in individual cells. 5. Single-cell immune profiling: A comprehensive approach to simultaneously examine the cellular context of the adaptive immune response and immune repertoires of T and B cells on a cell-by-cell basis. This approach can reveal insights into T and B cell variable (V), diversity (D), and joining (J) genes, known as V(D)J recombination, and immune cell profiling. 6. Spatial transcriptomics: An array containing capture probes is employed to bind RNA from tissue sections, and cDNA is then synthesized, followed by preparation of sequence libraries. The libraries are then sequenced, providing information on what genes are expressed, the changing quantities, and where the cells derive from. 7. Cell surface protein + SCS: This approach simultaneously measures both gene and cell surface protein expression in the same cell. As shown in the right panel of the figure, by applying bioinformatics tools and computational analysis, this SCS technology can reveal complex and rare cell populations, uncover regulatory relationships between genes, track the trajectories of distinct cell lineages in development, and many other applications