Sample demultiplexing, barcode processing and single-cell 3′ counting was performed using the Cell Ranger Single-Cell Software Suite (10x Genomics). Principal-component analysis (PCA) was performed using the top 3,000 most variable genes and t-distributed stochastic neighbour embedding (t-SNE) analysis was performed with the top 20 principal components. Clustering was performed using the FindClusters function, which works on k-nearest neighbour graph model with granularity ranging 0.1–0.9 and selected 0.4 for the downstream clustering. The quality control of mapped reads was performed using in-house scripts that employ Picard tools. Lipid extraction was performed using chloroform:methanol (2:1) (Folch extraction) as described previously71.