Single-Cell RNA Sequencing
Overview
Single-cell RNA sequencing (scRNA-seq) enables transcriptomic profiling at single-cell resolution, allowing identification of cell states, subtypes, and developmental trajectories within heterogeneous populations. When paired with single-cell TCR or BCR sequencing (e.g., 10x Genomics 5’ V(D)J), it enables simultaneous characterisation of gene expression and antigen receptor clonality.
Key Points from Literature
- scRNA-seq + scTCR-seq of activated CD4⁺ T cells in dengue: Ansari2025 performed 10x Genomics Chromium 5’ scRNA-seq + scTCR-seq on FACS-sorted CD38⁺HLA-DR⁺ CD4⁺ T cells from 4 acute dengue patients (4,361 cells total). This identified: (1) CXCR5⁺ Tfh-like cluster, (2) IL-21⁺ helper Tph, (3) GZMB⁺ cytotoxic Tph, and (4) regulatory/exhausted populations. Paired TCR data showed largely distinct clonotype usage between helper and cytotoxic Tph (only 13 shared clonotypes) (see Ansari2025 - Peripheral T Helper Subset Drives B Cell Response in Dengue, n=4 patients).
- Distinction from bulk RNA-seq: Prior studies in this wiki used bulk RNA-seq of sorted B cell populations (e.g., Jenks2018 - DN2 B Cells and EF Pathway in SLE — 2,154 DEGs across B cell subsets; Scharer2019 - Epigenetic Programming in SLE B Cells — 5,090 DEGs). scRNA-seq complements these by resolving heterogeneity within sorted populations but has lower per-cell gene detection sensitivity.
- 10x Genomics platform: The 10x Chromium system used in Ansari2025 is the same platform used for scV(D)J BCR sequencing in Woodruff2020 (ASC repertoire in COVID-19). The 5’ chemistry enables simultaneous gene expression + TCR/BCR sequencing from the same cell (see BCR Sequencing for the BCR application).
Contradictions & Debates
None documented in current wiki sources.
Related Pages
RNA Sequencing, BCR Sequencing, FACS Sorting, Peripheral Helper T Cell