Table 1.

Cell types in NeuroExpresso database

Cell type	Sample count	Marker gene count	GEO accession and reference
Whole brain
Astrocyte	9/1*	94**	GSE9566 (Cahoy et al., 2008), GSE35338 (Zamanian et al., 2012), GSE71585 (Tasic et al., 2016)
Oligodendrocyte	25/1*	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)
Microglia	3/1*	131**	GSE29949 (Anandasabapathy et al., 2011), GSE71585 (Tasic et al., 2016)
Cortex
FS Basket (G42)	13/5*	18	GSE17806 (Okaty et al., 2009), GSE8720 (Sugino et al., 2014), GSE2882 (Sugino et al., 2006), GSE71585 (Tasic et al., 2016)
Martinotti (GIN)	3/1*	15	GSE2882 (Sugino et al., 2006), GSE71585 (Tasic et al., 2016)
VIPReln (G30)	6/1*	33	GSE2882 (Sugino et al., 2006), GSE71585 (Tasic et al., 2016)
Pan-pyramidal***	9/17 *	35	See below
Pyramidal cortico-thalamic	3/2*	2	GSE2882 (Schmidt et al., 2012), GSE71585 (Tasic et al., 2016)
Pyramidal Glt25d2	3/2*	3	GSE35758 (Schmidt et al., 2012), GSE71585 (Tasic et al., 2016)
Pyramidal S100a10	3/4*	2	GSE35751 (Schmidt et al., 2012), GSE71585 (Tasic et al., 2016)
Layer 2 3 Pyra	2*	3	GSE71585 (Tasic et al., 2016)
Layer 4 Pyra	3*	5	GSE71585 (Tasic et al., 2016)
Layer 6a Pyra	2*	6	GSE71585 (Tasic et al., 2016)
Layer 6b Pyra	2*	9	GSE71585 (Tasic et al., 2016)
OPs	1*	184	GSE71585 (Tasic et al., 2016)
Endothelial	2*	178	GSE71585 (Tasic et al., 2016)
Basal forebrain
Forebrain cholinergic	3	90	GSE13379 (Doyle et al., 2008)
Striatum
Forebrain cholinergic	3	45	GSE13379 (Doyle et al., 2008)
Medium spiny neurons	39	74	GSE13379 (Doyle et al., 2008), GSE55096 (Heiman et al., 2014), GSE54656 (Maze et al., 2014), GSE48813 (Tan et al., 2013a)
Amygdala
Glutamatergic	3	10	GSE2882 (Sugino et al., 2006)
Pyramidal Thy1 Amyg	12	21	GSE2882 (Sugino et al., 2006)
Hippocampus
DentateGranule	3	17	GSE11147 (Perrone-Bizzozero et al., 2011)
GabaSSTReln	3	54	GSE2882 (Sugino et al., 2006)
Pyramidal Thy1 Hipp	12	17	GSE2882 (Sugino et al., 2006)
Subependymal
Ependymal	2	50	GSE18765 (Beckervordersandforth et al., 2010)
Thalamus
GabaReln	3	53	GSE2882 (Sugino et al., 2006)
Hypocretinergic	4	35	GSE38668 (Dalal et al., 2013)
Thalamus cholinergic	3	40	GSE43164 (Görlich et al., 2013)
Midbrain
Midbrain cholinergic	3	34	GSE13379 (Doyle et al., 2008)
Serotonergic	3	18	GSE36068 (Dougherty et al., 2013)
Substantia nigra
Dopaminergic	30	58**	No accession **** (Chung et al., 2005), GSE17542 (Phani et al., 2010)
Locus coeruleus
Noradrenergic	9	133	GSE8720 (Sugino et al., 2014), No accession**** (Sugino et al., unpublished observations)
Cerebellum
Basket	16	6	GSE13379 (Doyle et al., 2008), GSE37055 (Paul et al., 2012)
Bergmann	3	52	GSE13379 (Doyle et al., 2008)
Cerebellar granule cells	3	11	GSE13379 (Doyle et al., 2008)
Golgi	3	26	GSE13379 (Doyle et al., 2008)
Purkinje	44	43	GSE13379 (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 cholinergic	3	124	GSE13379 (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.