REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
Raw and analyzed data	https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE103322&format=file&file=GSE103322%5FHNSCC%5Fall%5Fdata%2Etxt%2Egz	GEO: GSE103322
Raw and analyzed data	https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE89567&format=file&file=GSE89567%5FIDH%5FA%5Fprocessed%5Fdata%2Etxt%2Egz	GEO: GSE89567
Raw and analyzed data	https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE108989	GEO: GSE108989
Raw and analyzed data	https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98638	GEO: GSE98638
Raw and analyzed data	https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE102130&format=file&file=GSE102130%5FK27Mproject%2ERSEM%2Evh20170621%2Etxt%2Egz	GEO: GSE102130
Raw and analyzed data	https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146771	GEO: GSE146771
Raw and analyzed data	https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE99254	GEO: GSE99254
Raw and analyzed data	https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE72056&format=file&file=GSE72056%5Fmelanoma%5Fsingle%5Fcell%5Frevised%5Fv2%2Etxt%2Egz	GEO: GSE72056
Raw and analyzed data	https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE115978	GEO: GSE115978
Raw and analyzed data	https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE70630&format=file&file=GSE70630%5FOG%5Fprocessed%5Fdata%5Fv2%2Etxt%2Egz	GEO: GSE70630
Raw count matrix of PBMC dataset	https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE96583	GEO: GSE96583
Raw count matrix of Muris dataset	https://figshare.com/projects/Tabula_Muris_Senis/64982	N/A
Software and algorithms
Seurat (v3.1.5)	(Butler et al., 2018)	https://satijalab.org/seurat/
Scanpy (v1.6.0)	(Wolf et al., 2018)	https://github.com/theislab/scanpy
scVI(v0.6.8)	(Lopez et al., 2018)	https://github.com/theislab/scvelo
limma (v3.34.9)		http://bioconductor.org/packages/release/bioc/html/limma.html