Table 3.
Summarization of RNA velocity applications across biological scenarios.
| Categories | Tissue/Cells | Biological implications | Algorithms | Key findings | Ref. |
|---|---|---|---|---|---|
| Differentiation and development | Mouse embryonic cells | Asynchronous emergence; multiple subpopulations | scVelo (deterministic) | Identified three neural crest cell subpopulations and validated cellular trajectories from E3.5 to E13.5. | [56] |
| Human forebrain | Rare population identification; temporal sequence; multiple developmental states | scVelo (dynamical) | Revealed temporal sequence of OPC specification and identified two distinct EGFR+ populations as OPC sources. | [53] | |
| Zebrafish neural stem cells | scRNA-Seq and scSLAM-Seq dual validation; alternative pathways; spatiotemporal diversity | scVelo (stochastic) Dynamo | Validated direct and proliferative differentiation trajectories. | [57] | |
| Zebrafish enteric nervous system | Neuronal subtype specification; spatiotemporal emergence patterns | scVelo (dynamical); UniTVelo | Identified distinct neuron subtypes with spatiotemporal emergence patterns. | [58] | |
| Human retina | Bidirectional development; multi-omic integration; temporal progression | scVelo (dynamical) MultiVelo (dynamical) | Revealed bidirectional developmental trajectories of retinal progenitor cells. | [55] | |
| Mouse medullary thymic epithelial cells | Branching development; precursor validation; experimental verification | scVelo (stochastic & dynamical) | Identified TAC-TECs as precursors to major mTEC subpopulations and predicted branching developmental model. | [59] | |
| Human bone marrow stromal cells | Hierarchical organization; multiple directions; driver gene identification | scVelo (stochastic) | Revealed two main developmental directions from MSSCs and identified key driver genes. | [60] | |
| Human Bone marrow | Lineage commitment; transitional progenitor states; NK cell ontogeny | scVelo (no model specified); TopicVelo | Identified transitional NK progenitors bridging HPCs and NK cells. | [51] | |
| Human B cells from multiple organs | Peripheral origin of thymic B cells; spatiotemporal B cell subset relationships | UniTVelo | Peripheral origin of thymic B cells confirmed by trajectory. | [61] | |
| Human subcutaneous adipose tissue | Active transitions; multiple sample types; scRNA-Seq and snRNA-seq analysis | scVelo (dynamical) | Validated adipocyte differentiation trajectories in WAT and SVF samples. | [62] | |
| Human small intestine | Sequential differentiation; unidirectional progression; stepwise maturation | scVelo (dynamical) | Mapped unidirectional cellular trajectory from stem cells to mature absorptive enterocytes. | [63] | |
| Human intestinal cells | Lineage differentiation; secretory cell specification; intracryptal maturation | CellDancer | Traced origin of differentiated intestinal cell types from intestinal stem cells. | [64] | |
| Human endometrial tissue | Epithelial-to-stromal transition |
scVelo
(dynamical), CellDancer |
Revealed disrupted epithelial-mesenchymal transition in preeclampsia patients. | [65] | |
| Human endometrial tissue | Luminal-to-glandular differentiation; endometrial regeneration | UniTVelo | Luminal cells show high differentiation potential toward glandular cells. | [66] | |
| Human fetal lung tissue | Progenitor differentiation | LatentVelo | Uncover unexpected cell lineage transitions in developing epithelium. | [67] | |
| Mouse testis (spermatocytes) | Meiotic progression; transcriptional dynamics in spermatogenesis |
scVelo (dynamical), UniTVelo |
Revealed stage-specific regulators guiding pachytene progression in spermatogenesis. | [68] | |
| Mouse visual cortex neurons | Stimulus-dependent transcriptional dynamics; vision-dependent circuit refinement during development | UniTVelo | Immediate early gene versus late response gene waves identified. | [69] | |
| Tomato callus | Sequential states; developmental relationships | scVelo (dynamical); Dynamo | Elucidated developmental trajectory among three shoot primordia subtypes. | [63] | |
| Diseases and injured microenvironments | Human & mouse monocytes | Early fate decision; alternative pathways; distinct lineages | scVelo (stochastic) | Revealed early bifurcation of monocytes into mo-DC and mo-Mac lineages. | [70] |
| Human peripheral blood mononuclear cells | Population heterogeneity; SLE patient variation; disease correlation | scVelo (no model specified) | Examined transcriptional heterogeneity in SLE patients. | [71] | |
| Human placentas | State transitions; disease-specific populations; developmental divergence | scVelo (dynamical) | Showed developmental stalling of preeclamptic trophoblasts. | [72] |
(continued)