Table 2.

Matching single-cell RNA sequencing data from tasic to well-defined cell types

Microarray cell type Tasic et al. (2016) cell clusterMatching methodNeuroExpresso cell type name
AstrocyteAstro Gja1Direct matchAstrocyte
MicrogliaMicro CtssDirect matchMicroglia
OligodendrocyteOligo OpalinDirect matchOligodendrocyte
FS Basket (G42)Pvalb Gpx3, Pvalb Rspo2, Pvalb Wt1, Pvalb Obox3, Pvalb Cpne5Definition: fast spiking pval positive interneuronsFS Basket (G42)
Martinotti (GIN)Sst Cbln4Direct matchMartinotti (GIN)
VIPReln (G30)Vip SncgUnique Vip and Sncg expression, high Sncg expression in microarray cell typeVIPReln (G30)
Pyramidal Glt25d2L5b Tph2, L5b Cdh13Definition: Glt25d2 positive Fam84b positivePyramidal Glt25d2
Pyramidal S100a10L5a Hsd11b1, L5a Batf3, L5a Tcerg1l, L5a Pde1cDefinition: S100a10 expressing cells from layer 5aPyramidal S100a10
Pyramidal CrtThalamicL6a Car12, L6a Syt17Direct matchPyramidal CrtThalamic
Endo Myl9, Endo Tbc1d4New cell typeEndothelial
OPC PdgfraNew cell typeOPCs
L4 Ctxn3, L4 Scnn1a, L4 Arf5New cell typeLayer 4 Pyra
L2 Ngb, L2/3 Ptgs2New cell typeLayer 2 3 Pyra
L6a Mgp, L6a SlaNew cell typeLayer 6a Pyra
L6b Serpinb11, L6b Rgs12New cell typeLayer 6b Pyra
  • List of molecular cell types identified by Tasic et al. (2016) and their corresponding cell types in NeuroExpresso. Matching method column defines how the matching was performed. Direct matches are one to one matching between the definition provided by Tasic et al. (2016) for the molecular cell types and definition provided by microarray samples. For “definition” matches, description of the cell type in the original source is used to find molecular cell types that fit the definition. VIPReln, Vip Sncg matching was done based on unique Sncg expression in VIPReln cells in the microarray data. New cell types are well defined cell types that have no counterpart in microarray data.