Methods: O’Leary et al 2020
Cell-types: Neurons (excitatory)
Brain regions: Basal and lateral amygdala
Techniques: Genetic labeling; manual cell-sorting to 8-well strips; selection-free cell-sampling; single-cell RNAseq with HiSeq 2500. 1,231 excitatory neurons were assigned to 6 cell-type (metacell) clusters (e.g. BA1).
Details of mice: C57BL/6 background; ≥8 weeks of age
Data processing for BrainPalmSeq: Single-cell counts were downloaded from GEO with accession ID GSE148866 (file GSE148866_combinedTables.txt) 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 for each gene, with the cluster identity for each cell provided by M.S. Cembrowski (private communication). Genes associated with palmitoylation were selected in order to create the heatmaps.
Heatmap units: mean log2(counts per 10,000 + 1)
References: O’leary, T.P., Sullivan, K.E., Wang, L., Clements, J., Lemire, A.L., and Cembrowski, M.S. (2020). Extensive and spatially variable within cell-type heterogeneity across the basolateral amygdala. ELife 9, 1–27.
Original data availability: GSE148866