Summary
This dataset contains 68,923 cells (38,958 neurons) collected from 8 samples of day 1 adult N2 hermaphrodites.
Data preparation
Cells were dissociated from adult hermaphrodites (Taylor et al. 2021; Taylor et al. 2024), fixed in methanol, and stored at -20 C for < 1 week. We stained methanol-fixed cells with DAPI and collected diploid cells (2N) using FACS; haploid (1N) germline cells were excluded (Roux et al. 2023). By collecting all diploid cells, rather than targeting populations of neurons marked with fluorescent markers as in our previous profile of L4 larval neurons (Taylor et al. 2021), we were able to capture the entire nervous system with a smaller number of samples. We generated libraries for sequencing using the 10X Genomics platform.
Cell type annotation
Neuronal clusters were annotated by comparing top markers to the L4 dataset.
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 | 0.855 | 0.238 |
| 2 | 0.813 | 0.200 |
| 3 | 0.699 | 0.151 |
| 4 | 0.579 | 0.117 |
REFERENCES
Roux AE, Yuan H, Podshivalova K, Hendrickson D, Kerr R, Kenyon C, Kelley D. 2023. Individual cell types in C . elegans age differently and activate distinct cell-protective responses. CellReports. 42(8):112902. doi:10.1016/j.celrep.2023.112902.
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.