GeneCore is the in-house genomics service centre at EMBL
Single-cell sequencing measures molecular profiles in individual cells, revealing cell-to-cell differences that bulk assays average out. Across laboratories, the main applications of scRNA-seq and scDNA-seq are broadly similar, since they are determined by what is being measured (RNA versus DNA). Practical differences usually come from sample preparation, platform and protocol choices, sequencing depth, and data analysis, which mainly influence sensitivity and resolution.
BD Rhapsody (Becton Dickinson) is a single-cell platform that captures individual cells in microwells and labels their RNA with cell-specific barcodes, enabling high-throughput gene expression (and compatible multiomic) profiling while linking sequencing reads back to each cell of origin.
10x Genomics Chromium is a droplet microfluidics platform that partitions single cells (or nuclei) into barcoded Gel-beads-in-emulsion (GEMs), enabling high-throughput single-cell sequencing by assigning sequencing reads back to their cell of origin via cell barcodes.
Smart-seq (e.g., Smart-seq2/3) is a plate-based single-cell RNA-seq method that generates full-length transcript libraries from individual cells, providing high per-cell sensitivity (useful for isoforms and allele-specific expression) but typically at lower throughput than droplet-based platforms.
Multiple Displacement Amplifications (MDA) is a single-cell DNA method that uses phi29 DNA polymerase to amplify the entire genome from a single cell before sequencing, enabling whole‑genome or exome analysis but often introducing coverage bias and allele dropout, which can affect variant calling.