Summary
This dataset contains 161,072 cells (89,073 neurons) collected from 16 samples of mid to late L1 hermaphrodites.
Data preparation
Cells were obtained from 10 different strains with various fluorescent neuronal markers (reporters listed in figure below). Cells were isolated as previously described (Taylor et al. 2021; Taylor et al. 2024). Live neurons expressing fluorescent markers were isolated using FACS. We generated libraries for sequencing using the 10X Genomics platform.
Cell type annotation
The L1 nervous system includes 91 classes of embryonically born neurons and 17 classes of neurons that derive from cell divisions during the mid to late L1 stage. Post-mitotic neuronal clusters were annotated by comparing top markers to the L4 dataset. We also captured many neuronal progenitors, identified by expression of cell cycle genes (e.g. cdk-1) and lineage-specific markers.
Thresholding
We performed dynamic thresholding as previously described (Taylor et al. 2021) and selected 4 thresholds of varying stringency
| Threshold | True positive rate | False discovery rate |
| 1 | 0.853 | 0.202 |
| 2 | 0.807 | 0.170 |
| 3 | 0.689 | 0.127 |
| 4 | 0.577 | 0.103 |
REFERENCES
Taylor SR, McWhirter RD, Matlock BK, Flaherty DK, Miller DM. 2024. Protocol for isolating specific C. elegans neuron types for bulk and single-cell RNA sequencing. STAR Protoc. 5(4):103439. doi:10.1016/j.xpro.2024.103439.
Taylor SR, Santpere G, Weinreb A, Barrett A, Reilly MB, Xu C, Varol E, Oikonomou P, Glenwinkel L, McWhirter R, et al. 2021. Molecular topography of an entire nervous system. Cell. 184(16):4329–4347. doi:10.1016/j.cell.2021.06.023.