# Single-cell RNA sequencing (scRNA-seq, 10x Chromium)

Source: https://onco.cc/terms/single-cell-rna-seq/  
OnCo record `single-cell-rna-seq` (Term). Data CC BY-NC 4.0, attribute "Data from OnCo (onco.cc)"; commercial use needs a licence.

## TL;DR

Single-cell RNA sequencing measures gene expression one cell at a time, revealing the cell types inside a tumour that bulk sequencing averages away.

## Summary

Single-cell transcriptomics is the quantification and analysis of the transcriptomes of individual cells, which makes it possible to unravel heterogeneous cell populations, reconstruct developmental pathways and model transcriptional dynamics (Wikipedia). Droplet platforms such as 10x Genomics Chromium capture thousands of cells per run; CELLxGENE and the Human Cell Atlas hold tens of millions of profiled cells and are the training data for single-cell foundation models. Pseudobulk, summing the cells of a sample, recovers a bulk-like profile for comparison. Single-cell data is sparse and normalised differently from bulk, so a model trained on one is out of distribution on the other.

## Fields

- Kind: Term
- Last checked: 2026-09-24
- Also known as: single-cell RNA-seq; scRNA-seq; single-cell RNA sequencing; single-cell transcriptomics; single-cell expression; 10x Chromium; Chromium single cell; pseudobulk
- Tags: cansim-terms

## Notes

- Listed in the CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme; CanSim page path /terms/single-cell-rna-seq.

## Sources

- Wikipedia: https://en.wikipedia.org/wiki/Single-cell_transcriptomics
- Wikipedia: https://en.wikipedia.org/wiki/Single-cell_transcriptomics

## Connected records

- collections: [CZ CELLxGENE / Human Cell Atlas](https://onco.cc/collections/cellxgene-hca/)
- companies: [10x Genomics](https://onco.cc/companies/10x-genomics/)
- terms: [AnnData and h5ad files](https://onco.cc/terms/anndata-h5ad/), [Bulk RNA sequencing (RNA-seq) and the full transcriptome](https://onco.cc/terms/bulk-rna-seq/), [Cancer AI vocabulary (CanSim terms map)](https://onco.cc/terms/cancer-ai-vocabulary/), [Foundation model](https://onco.cc/terms/foundation-model/), [Single-cell and transcriptome foundation models: UCE, GeneCompass, BulkFormer, BulkRNABert](https://onco.cc/terms/single-cell-foundation-models/), [Spatial transcriptomics platforms (Visium HD, Xenium, MERFISH, CosMx, CODEX)](https://onco.cc/terms/spatial-transcriptomics-platforms/), [Uberon anatomy ontology and the Cell Ontology](https://onco.cc/terms/uberon/), [Virtual cell models and in-silico perturbation screens](https://onco.cc/terms/virtual-cell-models/)
- technologies: [Single-cell & spatial profiling](https://onco.cc/technologies/single-cell-spatial/)

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