Table 1.

Cell types in NeuroExpresso database

Cell typeSample countMarker gene countGEO accession and reference
Whole brain
Astrocyte9/1*94**GSE9566 (Cahoy et al., 2008), GSE35338 (Zamanian et al., 2012), GSE71585 (Tasic et al., 2016)
Oligodendrocyte25/1*22**GSE48369, (Bellesi et al., 2013), GSE9566 (Cahoy et al., 2008), GSE13379 (Doyle et al., 2008), GSE30016 (Fomchenko et al., 2011), GSE71585 (Tasic et al., 2016)
Microglia3/1*131**GSE29949 (Anandasabapathy et al., 2011), GSE71585 (Tasic et al., 2016)
FS Basket (G42)13/5*18GSE17806 (Okaty et al., 2009), GSE8720 (Sugino et al., 2014), GSE2882 (Sugino et al., 2006), GSE71585 (Tasic et al., 2016)
Martinotti (GIN)3/1*15GSE2882 (Sugino et al., 2006), GSE71585 (Tasic et al., 2016)
VIPReln (G30)6/1*33GSE2882 (Sugino et al., 2006), GSE71585 (Tasic et al., 2016)
Pan-pyramidal***9/17 *35See below
Pyramidal cortico-thalamic3/2*2GSE2882 (Schmidt et al., 2012), GSE71585 (Tasic et al., 2016)
Pyramidal Glt25d23/2*3GSE35758 (Schmidt et al., 2012), GSE71585 (Tasic et al., 2016)
Pyramidal S100a103/4*2GSE35751 (Schmidt et al., 2012), GSE71585 (Tasic et al., 2016)
Layer 2 3 Pyra2*3GSE71585 (Tasic et al., 2016)
Layer 4 Pyra3*5GSE71585 (Tasic et al., 2016)
Layer 6a Pyra2*6GSE71585 (Tasic et al., 2016)
Layer 6b Pyra2*9GSE71585 (Tasic et al., 2016)
OPs1*184GSE71585 (Tasic et al., 2016)
Endothelial2*178GSE71585 (Tasic et al., 2016)
Basal forebrain
Forebrain cholinergic390GSE13379 (Doyle et al., 2008)
Forebrain cholinergic345GSE13379 (Doyle et al., 2008)
Medium spiny neurons3974GSE13379 (Doyle et al., 2008), GSE55096 (Heiman et al., 2014), GSE54656 (Maze et al., 2014), GSE48813 (Tan et al., 2013a)
Glutamatergic310GSE2882 (Sugino et al., 2006)
Pyramidal Thy1 Amyg1221GSE2882 (Sugino et al., 2006)
DentateGranule317GSE11147 (Perrone-Bizzozero et al., 2011)
GabaSSTReln354GSE2882 (Sugino et al., 2006)
Pyramidal Thy1 Hipp1217GSE2882 (Sugino et al., 2006)
Ependymal250GSE18765 (Beckervordersandforth et al., 2010)
GabaReln353GSE2882 (Sugino et al., 2006)
Hypocretinergic435GSE38668 (Dalal et al., 2013)
Thalamus cholinergic340GSE43164 (Görlich et al., 2013)
Midbrain cholinergic334GSE13379 (Doyle et al., 2008)
Serotonergic318GSE36068 (Dougherty et al., 2013)
Substantia nigra
Dopaminergic3058**No accession **** (Chung et al., 2005), GSE17542 (Phani et al., 2010)
Locus coeruleus
Noradrenergic9133GSE8720 (Sugino et al., 2014), No accession**** (Sugino et al., unpublished observations)
Basket166GSE13379 (Doyle et al., 2008), GSE37055 (Paul et al., 2012)
Bergmann352GSE13379 (Doyle et al., 2008)
Cerebellar granule cells311GSE13379 (Doyle et al., 2008)
Golgi326GSE13379 (Doyle et al., 2008)
Purkinje4443GSE13379 (Doyle et al., 2008), GSE57034 (Galloway et al., 2014), GSE37055 (Paul et al., 2012), no accession**** (Rossner et al., 2006), GSE8720 (Sugino et al., 2014), no accession**** Sugino et al. (unpublished observations)
Spinal cord
Spinal cord cholinergic3124GSE13379 (Doyle et al., 2008)
  • Sample count, number of samples that representing the cell type; gene count, number of marker genes detected for cell type; *, the number of clusters from RNA-seq data; **, marker genes for these cell types are identified in multiple regions displayed yet only the number of the genes that are found in the region specified on the table is shown for the sake of conservation of space. Astrocytes, microglia, and oligodendrocyte markers are identified in the context of all other brain regions (except cerebellum for astrocytes) and dopaminergic markers are also identified for midbrain; ***, pan-pyramidal is a merged cell type composed of all pyramidal samples; ****, data obtained directly from authors.