Methods: Zeisel et al 2015

Cell-types: All

Brain regions: Somatosensory Cortex (S1) & Hippocampus CA1

Techniques: Selection-free cell-sampling (except FACS sorting of 5HT3EGFP mice labeling GABAergic interneurons derived from the caudal ganglionic eminence). Single-cell RNAseq using Fluidigm C1.

Details of mice: Male and female; CD-1 background; P21-31.

Data processing for BrainPalmSeq: Single-cell counts were downloaded from, 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 cluster, tissue and class for each gene. Genes associated with palmitoylation were selected in order to create the heatmaps, categories comprising fewer than 5 single cells are not displayed.

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

References: Zeisel, A., M͡oz-Manchado, A.B., Codeluppi, S., Lönnerberg, P., Manno, G. La, Juréus, A., Marques, S., Munguba, H., He, L., Betsholtz, C., et al. (2015). Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science 347, 1138–1142.


Original data availability: GSE60361