Matching single-cell RNA sequencing data from tasic to well-defined cell types
| Microarray cell type | Tasic et al. (2016) cell cluster | Matching method | NeuroExpresso cell type name |
|---|---|---|---|
| Astrocyte | Astro Gja1 | Direct match | Astrocyte |
| Microglia | Micro Ctss | Direct match | Microglia |
| Oligodendrocyte | Oligo Opalin | Direct match | Oligodendrocyte |
| FS Basket (G42) | Pvalb Gpx3, Pvalb Rspo2, Pvalb Wt1, Pvalb Obox3, Pvalb Cpne5 | Definition: fast spiking pval positive interneurons | FS Basket (G42) |
| Martinotti (GIN) | Sst Cbln4 | Direct match | Martinotti (GIN) |
| VIPReln (G30) | Vip Sncg | Unique Vip and Sncg expression, high Sncg expression in microarray cell type | VIPReln (G30) |
| Pyramidal Glt25d2 | L5b Tph2, L5b Cdh13 | Definition: Glt25d2 positive Fam84b positive | Pyramidal Glt25d2 |
| Pyramidal S100a10 | L5a Hsd11b1, L5a Batf3, L5a Tcerg1l, L5a Pde1c | Definition: S100a10 expressing cells from layer 5a | Pyramidal S100a10 |
| Pyramidal CrtThalamic | L6a Car12, L6a Syt17 | Direct match | Pyramidal CrtThalamic |
| — | Endo Myl9, Endo Tbc1d4 | New cell type | Endothelial |
| — | OPC Pdgfra | New cell type | OPCs |
| — | L4 Ctxn3, L4 Scnn1a, L4 Arf5 | New cell type | Layer 4 Pyra |
| — | L2 Ngb, L2/3 Ptgs2 | New cell type | Layer 2 3 Pyra |
| — | L6a Mgp, L6a Sla | New cell type | Layer 6a Pyra |
| — | L6b Serpinb11, L6b Rgs12 | New cell type | Layer 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.