About
An interactive tool for exploring translational regulation in the early C. elegans embryo (1- to 8-cell stage).
Data Sources
| Dataset | Source | What it measures |
|---|---|---|
| TE, Ribo, RNA | Shukla et al. 2025, Cell Reports | Ribosome occupancy & mRNA abundance per stage (CLR-normalized, batch-corrected) |
| Spatial mRNA | Tintori et al. 2016, Developmental Cell | Per-cell transcript abundance at blastomere resolution |
Gene set: 4,905 genes passing CPM filters in both Ribo-seq and RNA-seq.
How to Read the Plots
Top Panels — TE, Ribosome Occupancy & mRNA
Left — Translational Efficiency (TE)
- TE = Ribosome CLR − mRNA CLR (log-ratio of ribosome footprints to mRNA)
- Positive = translated more efficiently than average. Negative = translationally repressed.
- Grey dashed lines are reference genes: lem-2 (high TE), gpd-4 (housekeeping), nos-2 (low TE, repressed)
Right — Ribosome Occupancy & mRNA Abundance
- Orange = ribosome occupancy. Blue = mRNA abundance.
- Lines diverging → translational regulation. Lines converging → mRNA-driven change.
Bottom Panel — Spatial mRNA (Embryo Pictogram)
- Darker = more mRNA in that cell. Asymmetric coloring = mRNA is localized.
- Cells at each stage: P0 → AB/P1 → ABa/ABp/EMS/P2 → ABal/ABar/ABpl/ABpr/MS/E/C/P3
- This shows mRNA only, not where translation occurs.
Disclaimer: This embryo visualization was re-created from the original DrEdGE tool by Sophie Tintori, tintori.bio.unc.edu. Please refer to that site to explore and access the full per-cell RNA expression data.
Gene Names
The TE data uses common names (par-3, nos-2). The Tintori data uses systematic names (F54E7.3). This tool maps between them automatically via WormBase aliases. If the spatial panel shows "not found," no alias exists for that gene.
Tools
The ribosome profiling data was processed using RiboFlow — a software ecosystem for ribosome profiling that works at footprint-length resolution. It includes a pipeline (RiboFlow) and two interfaces (RiboR, RiboPy).
Citation
Shukla et al. (2025). Landscape and regulation of mRNA translation in the early C. elegans embryo. Cell Reports, 44(4).
Tintori et al. (2016). A Transcriptional Lineage of the Early C. elegans Embryo. Developmental Cell, 38(4).