Summary
This dataset contains 100,955 cells collected from 17 samples of L4 hermaphrodites.
Data preparation
Details available in accompanying publication (Taylor et al., 2021).
Cell type annotation
Clusters were annotated based on the expression on marker genes detailed in the accompanying publication (Taylor et al., 2021), table S1B.
Thresholding
The dynamic thresholding is described in the accompanying publication (Taylor et al., 2021). Thresholding was used to determine if a gene was expressed in a cell or not. We offer expression levels at four different thresholds. Threshold 1 is the least stringent and has the highest numbers of expressed genes per neuron type, at the risk of some possible false positives. Threshold 4 is the most stringent, with the fewest genes detected per neuron type. This reduces false positives at the cost of increased false negatives. We feel threshold 2 offers a good balance. See the preprint (Methods and Figure S6) for more details. The true positive rates and false discovery rates for the 4 thresholds are:
| Threshold | True Positive Rate | False Discovery Rate |
| 1 | 0.853 | 0.197 |
| 2 | 0.810 | 0.140 |
| 3 | 0.696 | 0.104 |
| 4 | 0.582 | 0.084 |
Genes with unreliable expression
Several transgenic worm strains were used to isolate neurons for scRNA-seq. The transgenes used to generate these strains often lead to overexpression of genes. The following genes show both ectopic expression and overexpression (OE): unc-54 (the unc-54 3’ UTR is used for all but one of the strains used), dpy-20, rol-6, lin-15A, lin-15B, unc-119, pha-1 (all full-length OE in rescue constructs), F38B6.2, C30F8.3, cex-1, C30A5.16, and saeg-2 (regions of these genes are included in promoter sequences for some strains).
Five additional genes are over-expressed under the control of endogenous regulatory elements: eat-4, cho-1, unc-53, unc-47 and gcy-35. These genes have inflated expression levels, but do not show ectopic expression.
There are also additional genes that are likely induced by dissociation-related cellular stress. A list is available below.
REFERENCES
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.