Methods: Kozareva et al 2020
Brain regions: Cerebellum
Techniques: Selection-free cell-sampling. Single-cell RNAseq using droplet microfluidics (10X Genomics Chromium). A total of 611,034 single-nuclei were assigned to 46 cell-type (metacell) clusters (e.g. Astrocyte_1).
Details of mice: Male and female; C57BL/6J background; P60
Data processing for BrainPalmSeq: For Kozareva single-cell counts were downloaded from https://singlecell.broadinstitute.org/single_cell/study/SCP795/ (Seurat R file cb_annotated_object.RDS), 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 subcluster for each gene. Genes associated with palmitoylation were selected in order to create the heatmap. The top 5 marker genes for each subcluster were obtained directly from the published results (Supplementary Table 2 from Kozareva et al.).
Heatmap units: mean log2(counts per 10,000 + 1)
References: Velina Kozareva, Caroline Martin, Tomas Osorno, Stephanie Rudolph, Chong Guo, Charles Vanderburg, Naeem Nadaf, Aviv Regev, Wade G. Regehr & Evan Macosko (2021). A transcriptomic atlas of mouse cerebellar cortex comprehensively defines cell types.
Original data availability: https://singlecell.broadinstitute.org/single_cell/study/SCP795/