Methods: Zeisel et al 2018 “MouseBrain”

Cell-types: All

Brain regions: Central nervous system (CNS; Olfactory bulb; Cortex; Striatum; Amygdala; Hypothalamus; Thalamus; Hippocampus; Midbrain; Cerebellum; Pons; Medulla), Peripheral nervous system (PNS; Spinal Cord; Sympathetic chain), Enteric nervous system (ENS; Myenteric plexus; Muscle layer; Submucosal plexus).

Techniques: Selection-free cell-sampling (except FACS sorting of ENS neural-crest-derived cells with Wnt1-Cre;R26Tomato transgenic mice and hippocampal inhibitory neurons with vGat-Cre;TdTomato mice). Single-cell RNAseq using droplet microfluidics (10X Genomics Chromium). 160,796 cells were assigned to 265 cell-type (metacell) clusters (e.g. TEGLU1).

Age of mice: P12-30; 6 weeks; 8 weeks

Data processing for BrainPalmSeq: Single-cell counts were downloaded from (loom file named l5_all.loom), and log normalized by first scaling the expression values provided to a sum of 10,000 per cell before calculating log2(scaled_counts+1). Averages were then performed by brain region, neurotransmitter and taxonomy for each gene. Genes associated with palmitoylation were selected in order to create the heatmaps.

Heatmap units: mean log2(counts per 10,000 + 1)


Zeisel, A., Hochgerner, H., Lönnerberg, P., Johnsson, A., Memic, F., van der Zwan, J., Häring, M., Braun, E., Borm, L.E., La Manno, G., et al. (2018). Molecular Architecture of the Mouse Nervous System. Cell 174, 999-1014.e22.


Original data availability: