Figure S1.

Comparison of Two Different Filtering Cutoffs, Related to Figure 1

(A–C) SCENIC t-SNEs of the 157K dataset (lenient filtering) colored by (A) VAChT indicating cholinergic neurons in blue, VGlut indicating glutamatergic neurons in green and Gad1 indicating GABAergic neurons in red, (B) elav indicating neurons in green and repo indicating glia in red, (C) lncRNA:noe indicating neurons in green and lncRNA:CR34335 indicating glia in red.

(D–F) SCENIC t-SNEs of the 57K dataset (stringent filtering), with aforementioned colors.

(G) Plots per 10x Chromium run indicating the cumulative fraction of UMIs, red dots indicate Cell Ranger cutoffs used for the 57K dataset (note that additional filtering by Scater was applied after the Cell Ranger cutoff), blue dots indicate our less stringent cutoffs used for the 157K dataset