Methods: Gokce et al 2016
Brain regions: Striatum
Techniques: Genetic labeling of medium spiny neurons (D1-tdTomato (tdTom)/D2-GFP) and astrocytes (Aldh1l1-GFP mice), single-cell RNAseq with FACS-scRNA-seq; selection free sampling with microfluidic single-cell RNAseq. 1,208 single-cells were assigned to 10 cell-type (metacell) clusters (e.g. Astro).
Details of mice: Male mice; C57Bl/6 background; 5- to 7-week-old
Data processing for BrainPalmSeq: Single-cell data were downloaded from GEO with accession ID GSE82187 (file GSE82187_cast_all_forGEO.csv). Counts were log normalized by first scaling to a sum of 10,000 per cell before calculating log2(scaled_counts+1). Averages were then performed by cell type for each gene. Genes associated with palmitoylation were selected in order to create the heatmaps.
Heatmap units: mean log2(counts per 10,000 + 1)
References: Gokce, O., Stanley, G.M., Treutlein, B., Neff, N.F., Camp, J.G., Malenka, R.C., Rothwell, P.E., Fuccillo, M. V., Südhof, T.C., and Quake, S.R. (2016). Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq. Cell Reports 16, 1126–1137
Original data availability: GSE82187