Single nuclei brain data

Brain regions

Brain region
Data source
Cell count
Total read count
Amygdalalinnarsson1871653778826743
Basal ganglialinnarsson2959484518978066
Cerebellumlinnarsson151940800654566
Cerebral cortexlinnarsson5000009279411261
Hippocampuslinnarsson3479396452849485
Hypothalamuslinnarsson1344302531751407
Medulla oblongatalinnarsson85435657979524
Midbrainlinnarsson2492782548432382
Ponslinnarsson2041102209879371
Spinal cordlinnarsson24183139672409
Thalamuslinnarsson3432975756585457
Download: rna_single_nuclei_brain_datasets.tsv.zip | 11 lines

Cluster type data

Transcript expression levels summarized per gene in 34 cluster types from 11 brain regions. The tab-separated file includes Ensembl gene identifier ("Gene"), gene name ("Gene name"), analysed sample ("Cluster type") and normalized expresion ("nTPM").

Cluster types

Cluster type
Cell type group
amygdala excitatoryNeuronal cells
astrocyteGlial cells
bergmann gliaGlial cells
central nervous system macrophageGlial cells
cerebellar inhibitoryNeuronal cells
CGE interneuronNeuronal cells
choroid plexus epithelial cellGlial cells
committed oligodendrocyte precursorGlial cells
deep-layer corticothalamic and 6bNeuronal cells
deep-layer intratelencephalicNeuronal cells
deep-layer near-projectingNeuronal cells
eccentric medium spiny neuronNeuronal cells
endothelial cellEndothelial cells
ependymal cellGlial cells
fibroblastMesenchymal cells
hippocampal CA1-3Neuronal cells
hippocampal CA4Neuronal cells
hippocampal dentate gyrusNeuronal cells
LAMP5-LHX6 and ChandelierNeuronal cells
leukocyteBlood & immune cells
lower rhombic lipNeuronal cells
mammillary bodyNeuronal cells
medium spiny neuronNeuronal cells
MGE interneuronNeuronal cells
midbrain-derived inhibitoryNeuronal cells
miscellaneousNeuronal cells
oligodendrocyteGlial cells
oligodendrocyte precursor cellGlial cells
pericyteMuscle cells
splatterNeuronal cells
thalamic excitatoryNeuronal cells
upper rhombic lipNeuronal cells
upper-layer intratelencephalicNeuronal cells
vascular associated smooth muscle cellMuscle cells
Download: rna_single_nuclei_cluster_type_cluster_types.tsv.zip | 34 lines

Cluster data

Transcript expression levels summarized per gene and cluster in 260 clusters. The tab-separated file includes Ensembl gene identifier ("Gene"), gene name ("Gene name"), tissue ("Tissue"), analysed sample ("Cell type"), cluster ("Cluster"), read count ("Read count") and normalized expression ("nTPM").

Brain region
Cluster
Cluster type
Cell type group
Cell count
Included in aggregation
Amygdalac-0Upper rhombic lipNeuronal cells22No
Amygdalac-1SplatterNeuronal cells7659Yes
Amygdalac-2Amygdala excitatoryNeuronal cells61749Yes
Amygdalac-3Medium spiny neuronNeuronal cells7324Yes
Amygdalac-4Eccentric medium spiny neuronNeuronal cells13706Yes
Amygdalac-5Midbrain-derived inhibitoryNeuronal cells37Yes
Amygdalac-6Cge interneuronNeuronal cells21317Yes
Amygdalac-7Lamp5-lhx6 and chandelierNeuronal cells6288Yes
Amygdalac-8Mge interneuronNeuronal cells7826Yes
Amygdalac-9Deep-layer near-projectingNeuronal cells221Yes
Amygdalac-10Deep-layer corticothalamic and 6bNeuronal cells4705Yes
Amygdalac-11MiscellaneousNeuronal cells725Yes
Amygdalac-12Hippocampal ca1-3Neuronal cells1039Yes
Amygdalac-13Upper-layer intratelencephalicNeuronal cells4331Yes
Amygdalac-14Deep-layer intratelencephalicNeuronal cells17219Yes
Amygdalac-15LeukocyteBlood & immune cells86Yes
Amygdalac-16OligodendrocyteGlial cells14173Yes
Amygdalac-17Committed oligodendrocyte precursorGlial cells466Yes
Amygdalac-18AstrocyteGlial cells7503Yes
Amygdalac-19Oligodendrocyte precursor cellGlial cells6413Yes
Amygdalac-20Ependymal cellGlial cells255Yes
Amygdalac-21FibroblastMesenchymal cells263Yes
Amygdalac-22PericyteMuscle cells79Yes
Amygdalac-23Vascular associated smooth muscle cellMuscle cells32Yes
Amygdalac-24Endothelial cellEndothelial cells202Yes
Amygdalac-25Central nervous system macrophageGlial cells3525Yes
Basal gangliac-0Upper rhombic lipNeuronal cells150Yes
Basal gangliac-1SplatterNeuronal cells31151Yes
Basal gangliac-2Lower rhombic lipNeuronal cells899Yes
Basal gangliac-3Thalamic excitatoryNeuronal cells479Yes
Basal gangliac-4Amygdala excitatoryNeuronal cells348Yes
Basal gangliac-5Medium spiny neuronNeuronal cells125373Yes
Basal gangliac-6Eccentric medium spiny neuronNeuronal cells16958Yes
Basal gangliac-7Midbrain-derived inhibitoryNeuronal cells236Yes
Basal gangliac-8Cge interneuronNeuronal cells4106Yes
Basal gangliac-9Lamp5-lhx6 and chandelierNeuronal cells975Yes
Basal gangliac-10Mge interneuronNeuronal cells2537Yes
Basal gangliac-11Deep-layer near-projectingNeuronal cells538Yes
Basal gangliac-12Deep-layer corticothalamic and 6bNeuronal cells1046Yes
Basal gangliac-13MiscellaneousNeuronal cells245Yes
Basal gangliac-14Upper-layer intratelencephalicNeuronal cells2089Yes
Basal gangliac-15Deep-layer intratelencephalicNeuronal cells2564Yes
Basal gangliac-16LeukocyteBlood & immune cells477Yes
Basal gangliac-17OligodendrocyteGlial cells49797Yes
Basal gangliac-18Committed oligodendrocyte precursorGlial cells446Yes
Basal gangliac-19AstrocyteGlial cells19208Yes
Basal gangliac-20Oligodendrocyte precursor cellGlial cells7559Yes
Basal gangliac-21Ependymal cellGlial cells1217Yes
Basal gangliac-22Choroid plexus epithelial cellGlial cells6116Yes
Basal gangliac-23FibroblastMesenchymal cells1191Yes
Basal gangliac-24PericyteMuscle cells370Yes
Basal gangliac-25Vascular associated smooth muscle cellMuscle cells112Yes
Basal gangliac-26Endothelial cellEndothelial cells315Yes
Basal gangliac-27Central nervous system macrophageGlial cells19446Yes
Cerebellumc-0Upper rhombic lipNeuronal cells89111Yes
Cerebellumc-1Lower rhombic lipNeuronal cells10No
Cerebellumc-2SplatterNeuronal cells1743Yes
Cerebellumc-3MiscellaneousNeuronal cells11No
Cerebellumc-4Cerebellar inhibitoryNeuronal cells11720Yes
Cerebellumc-5Midbrain-derived inhibitoryNeuronal cells34Yes
Cerebellumc-6LeukocyteBlood & immune cells310Yes
Cerebellumc-7OligodendrocyteGlial cells22406Yes
Cerebellumc-8Committed oligodendrocyte precursorGlial cells77Yes
Cerebellumc-9AstrocyteGlial cells6578Yes
Cerebellumc-10Bergmann gliaGlial cells7703Yes
Cerebellumc-11Oligodendrocyte precursor cellGlial cells6155Yes
Cerebellumc-12Ependymal cellGlial cells18No
Cerebellumc-13FibroblastMesenchymal cells424Yes
Cerebellumc-14PericyteMuscle cells268Yes
Cerebellumc-15Vascular associated smooth muscle cellMuscle cells24No
Cerebellumc-16Endothelial cellEndothelial cells372Yes
Cerebellumc-17Central nervous system macrophageGlial cells4976Yes
Cerebral cortexc-0OligodendrocyteGlial cells27020Yes
Cerebral cortexc-1Committed oligodendrocyte precursorGlial cells324Yes
Cerebral cortexc-2AstrocyteGlial cells15988Yes
Cerebral cortexc-3Oligodendrocyte precursor cellGlial cells9773Yes
Cerebral cortexc-4FibroblastMesenchymal cells442Yes
Cerebral cortexc-5PericyteMuscle cells177Yes
Cerebral cortexc-6Vascular associated smooth muscle cellMuscle cells54Yes
Cerebral cortexc-7Endothelial cellEndothelial cells496Yes
Cerebral cortexc-8Central nervous system macrophageGlial cells5375Yes
Cerebral cortexc-9Upper rhombic lipNeuronal cells44Yes
Cerebral cortexc-10SplatterNeuronal cells1773Yes
Cerebral cortexc-11Thalamic excitatoryNeuronal cells33Yes
Cerebral cortexc-12Amygdala excitatoryNeuronal cells14762Yes
Cerebral cortexc-13Medium spiny neuronNeuronal cells3073Yes
Cerebral cortexc-14Eccentric medium spiny neuronNeuronal cells1754Yes
Cerebral cortexc-15Cge interneuronNeuronal cells62711Yes
Cerebral cortexc-16Lamp5-lhx6 and chandelierNeuronal cells10556Yes
Cerebral cortexc-17Mge interneuronNeuronal cells71085Yes
Cerebral cortexc-18Deep-layer near-projectingNeuronal cells6630Yes
Cerebral cortexc-19Deep-layer corticothalamic and 6bNeuronal cells22467Yes
Cerebral cortexc-20MiscellaneousNeuronal cells4262Yes
Cerebral cortexc-21Hippocampal ca1-3Neuronal cells228Yes
Cerebral cortexc-22Upper-layer intratelencephalicNeuronal cells164560Yes
Cerebral cortexc-23Deep-layer intratelencephalicNeuronal cells76239Yes
Cerebral cortexc-24LeukocyteBlood & immune cells174Yes
Hippocampusc-0Upper rhombic lipNeuronal cells15No
Hippocampusc-1SplatterNeuronal cells794Yes
Hippocampusc-2Amygdala excitatoryNeuronal cells5493Yes
Hippocampusc-3Eccentric medium spiny neuronNeuronal cells156Yes
Hippocampusc-4Cge interneuronNeuronal cells27319Yes
Hippocampusc-5Lamp5-lhx6 and chandelierNeuronal cells8066Yes
Hippocampusc-6Mge interneuronNeuronal cells17787Yes
Hippocampusc-7Medium spiny neuronNeuronal cells490Yes
Hippocampusc-8Deep-layer near-projectingNeuronal cells234Yes
Hippocampusc-9Deep-layer corticothalamic and 6bNeuronal cells12280Yes
Hippocampusc-10MiscellaneousNeuronal cells7317Yes
Hippocampusc-11Hippocampal ca1-3Neuronal cells73235Yes
Hippocampusc-12Upper-layer intratelencephalicNeuronal cells3124Yes
Hippocampusc-13Deep-layer intratelencephalicNeuronal cells4022Yes
Hippocampusc-14Hippocampal dentate gyrusNeuronal cells66837Yes
Hippocampusc-15Hippocampal ca4Neuronal cells10551Yes
Hippocampusc-16LeukocyteBlood & immune cells239Yes
Hippocampusc-17OligodendrocyteGlial cells49888Yes
Hippocampusc-18Committed oligodendrocyte precursorGlial cells594Yes
Hippocampusc-19AstrocyteGlial cells27778Yes
Hippocampusc-20Oligodendrocyte precursor cellGlial cells16581Yes
Hippocampusc-21Ependymal cellGlial cells1929Yes
Hippocampusc-22Choroid plexus epithelial cellGlial cells68Yes
Hippocampusc-23FibroblastMesenchymal cells685Yes
Hippocampusc-24PericyteMuscle cells249Yes
Hippocampusc-25Vascular associated smooth muscle cellMuscle cells65Yes
Hippocampusc-26Endothelial cellEndothelial cells850Yes
Hippocampusc-27Central nervous system macrophageGlial cells11293Yes
Hypothalamusc-0Upper rhombic lipNeuronal cells105Yes
Hypothalamusc-1SplatterNeuronal cells70808Yes
Hypothalamusc-2Mammillary bodyNeuronal cells16571Yes
Hypothalamusc-3Amygdala excitatoryNeuronal cells1919Yes
Hypothalamusc-4Medium spiny neuronNeuronal cells6995Yes
Hypothalamusc-5Eccentric medium spiny neuronNeuronal cells3337Yes
Hypothalamusc-6Midbrain-derived inhibitoryNeuronal cells2242Yes
Hypothalamusc-7Cge interneuronNeuronal cells2226Yes
Hypothalamusc-8Lamp5-lhx6 and chandelierNeuronal cells651Yes
Hypothalamusc-9Mge interneuronNeuronal cells1407Yes
Hypothalamusc-10Deep-layer near-projectingNeuronal cells175Yes
Hypothalamusc-11Deep-layer corticothalamic and 6bNeuronal cells277Yes
Hypothalamusc-12MiscellaneousNeuronal cells338Yes
Hypothalamusc-13Upper-layer intratelencephalicNeuronal cells2396Yes
Hypothalamusc-14Deep-layer intratelencephalicNeuronal cells581Yes
Hypothalamusc-15LeukocyteBlood & immune cells214Yes
Hypothalamusc-16OligodendrocyteGlial cells10646Yes
Hypothalamusc-17Committed oligodendrocyte precursorGlial cells443Yes
Hypothalamusc-18AstrocyteGlial cells5366Yes
Hypothalamusc-19Oligodendrocyte precursor cellGlial cells3353Yes
Hypothalamusc-20Ependymal cellGlial cells216Yes
Hypothalamusc-21FibroblastMesenchymal cells417Yes
Hypothalamusc-22PericyteMuscle cells78Yes
Hypothalamusc-23Vascular associated smooth muscle cellMuscle cells117Yes
Hypothalamusc-24Endothelial cellEndothelial cells189Yes
Hypothalamusc-25Central nervous system macrophageGlial cells3363Yes
Medulla oblongatac-0Upper rhombic lipNeuronal cells18335Yes
Medulla oblongatac-1SplatterNeuronal cells25408Yes
Medulla oblongatac-2Lower rhombic lipNeuronal cells2497Yes
Medulla oblongatac-3MiscellaneousNeuronal cells15No
Medulla oblongatac-4Cerebellar inhibitoryNeuronal cells728Yes
Medulla oblongatac-5Midbrain-derived inhibitoryNeuronal cells79Yes
Medulla oblongatac-6LeukocyteBlood & immune cells238Yes
Medulla oblongatac-7OligodendrocyteGlial cells22750Yes
Medulla oblongatac-8Committed oligodendrocyte precursorGlial cells120Yes
Medulla oblongatac-9AstrocyteGlial cells5497Yes
Medulla oblongatac-10Bergmann gliaGlial cells149Yes
Medulla oblongatac-11Oligodendrocyte precursor cellGlial cells2697Yes
Medulla oblongatac-12Ependymal cellGlial cells931Yes
Medulla oblongatac-13Choroid plexus epithelial cellGlial cells1435Yes
Medulla oblongatac-14FibroblastMesenchymal cells585Yes
Medulla oblongatac-15PericyteMuscle cells192Yes
Medulla oblongatac-16Vascular associated smooth muscle cellMuscle cells132Yes
Medulla oblongatac-17Endothelial cellEndothelial cells374Yes
Medulla oblongatac-18Central nervous system macrophageGlial cells3273Yes
Midbrainc-0Upper rhombic lipNeuronal cells9277Yes
Midbrainc-1SplatterNeuronal cells82161Yes
Midbrainc-2Lower rhombic lipNeuronal cells236Yes
Midbrainc-3Thalamic excitatoryNeuronal cells3069Yes
Midbrainc-4Amygdala excitatoryNeuronal cells17No
Midbrainc-5MiscellaneousNeuronal cells1194Yes
Midbrainc-6Cerebellar inhibitoryNeuronal cells326Yes
Midbrainc-7Midbrain-derived inhibitoryNeuronal cells29336Yes
Midbrainc-8Cge interneuronNeuronal cells707Yes
Midbrainc-9Lamp5-lhx6 and chandelierNeuronal cells125Yes
Midbrainc-10Mge interneuronNeuronal cells173Yes
Midbrainc-11Deep-layer corticothalamic and 6bNeuronal cells63Yes
Midbrainc-12Upper-layer intratelencephalicNeuronal cells193Yes
Midbrainc-13Deep-layer intratelencephalicNeuronal cells19No
Midbrainc-14Hippocampal dentate gyrusNeuronal cells362Yes
Midbrainc-15Hippocampal ca4Neuronal cells51Yes
Midbrainc-16LeukocyteBlood & immune cells516Yes
Midbrainc-17OligodendrocyteGlial cells80202Yes
Midbrainc-18Committed oligodendrocyte precursorGlial cells175Yes
Midbrainc-19AstrocyteGlial cells13278Yes
Midbrainc-20Bergmann gliaGlial cells29No
Midbrainc-21Oligodendrocyte precursor cellGlial cells11894Yes
Midbrainc-22Ependymal cellGlial cells276Yes
Midbrainc-23FibroblastMesenchymal cells710Yes
Midbrainc-24PericyteMuscle cells256Yes
Midbrainc-25Vascular associated smooth muscle cellMuscle cells108Yes
Midbrainc-26Endothelial cellEndothelial cells285Yes
Midbrainc-27Central nervous system macrophageGlial cells14240Yes
Ponsc-0Upper rhombic lipNeuronal cells19040Yes
Ponsc-1SplatterNeuronal cells33128Yes
Ponsc-2Lower rhombic lipNeuronal cells48985Yes
Ponsc-3MiscellaneousNeuronal cells14No
Ponsc-4Cerebellar inhibitoryNeuronal cells1559Yes
Ponsc-5Midbrain-derived inhibitoryNeuronal cells3770Yes
Ponsc-6LeukocyteBlood & immune cells487Yes
Ponsc-7OligodendrocyteGlial cells64564Yes
Ponsc-8Committed oligodendrocyte precursorGlial cells169Yes
Ponsc-9AstrocyteGlial cells10539Yes
Ponsc-10Bergmann gliaGlial cells149Yes
Ponsc-11Oligodendrocyte precursor cellGlial cells11865Yes
Ponsc-12Ependymal cellGlial cells425Yes
Ponsc-13Choroid plexus epithelial cellGlial cells20No
Ponsc-14FibroblastMesenchymal cells1008Yes
Ponsc-15PericyteMuscle cells469Yes
Ponsc-16Vascular associated smooth muscle cellMuscle cells90Yes
Ponsc-17Endothelial cellEndothelial cells507Yes
Ponsc-18Central nervous system macrophageGlial cells7322Yes
Spinal cordc-0Upper rhombic lipNeuronal cells859Yes
Spinal cordc-1SplatterNeuronal cells4910Yes
Spinal cordc-2Cerebellar inhibitoryNeuronal cells44Yes
Spinal cordc-3LeukocyteBlood & immune cells219Yes
Spinal cordc-4OligodendrocyteGlial cells11503Yes
Spinal cordc-5Committed oligodendrocyte precursorGlial cells44Yes
Spinal cordc-6AstrocyteGlial cells2435Yes
Spinal cordc-7Bergmann gliaGlial cells7No
Spinal cordc-8Oligodendrocyte precursor cellGlial cells1970Yes
Spinal cordc-9Ependymal cellGlial cells147Yes
Spinal cordc-10FibroblastMesenchymal cells68Yes
Spinal cordc-11PericyteMuscle cells78Yes
Spinal cordc-12Vascular associated smooth muscle cellMuscle cells8No
Spinal cordc-13Endothelial cellEndothelial cells215Yes
Spinal cordc-14Central nervous system macrophageGlial cells1676Yes
Thalamusc-0Upper rhombic lipNeuronal cells132Yes
Thalamusc-1SplatterNeuronal cells29251Yes
Thalamusc-2Thalamic excitatoryNeuronal cells81897Yes
Thalamusc-3Amygdala excitatoryNeuronal cells171Yes
Thalamusc-4Medium spiny neuronNeuronal cells3700Yes
Thalamusc-5Eccentric medium spiny neuronNeuronal cells1314Yes
Thalamusc-6Midbrain-derived inhibitoryNeuronal cells91033Yes
Thalamusc-7Cge interneuronNeuronal cells3337Yes
Thalamusc-8Lamp5-lhx6 and chandelierNeuronal cells740Yes
Thalamusc-9Mge interneuronNeuronal cells346Yes
Thalamusc-10Deep-layer corticothalamic and 6bNeuronal cells9No
Thalamusc-11MiscellaneousNeuronal cells36Yes
Thalamusc-12Upper-layer intratelencephalicNeuronal cells83Yes
Thalamusc-13Deep-layer intratelencephalicNeuronal cells17No
Thalamusc-14Hippocampal dentate gyrusNeuronal cells314Yes
Thalamusc-15Hippocampal ca4Neuronal cells11No
Thalamusc-16LeukocyteBlood & immune cells488Yes
Thalamusc-17OligodendrocyteGlial cells91385Yes
Thalamusc-18Committed oligodendrocyte precursorGlial cells1351Yes
Thalamusc-19AstrocyteGlial cells13648Yes
Thalamusc-20Oligodendrocyte precursor cellGlial cells10695Yes
Thalamusc-21Ependymal cellGlial cells467Yes
Thalamusc-22Choroid plexus epithelial cellGlial cells39Yes
Thalamusc-23FibroblastMesenchymal cells2566Yes
Thalamusc-24PericyteMuscle cells1171Yes
Thalamusc-25Vascular associated smooth muscle cellMuscle cells249Yes
Thalamusc-26Endothelial cellEndothelial cells654Yes
Thalamusc-27Central nervous system macrophageGlial cells8193Yes
Download: rna_single_nuclei_brain_clusters.tsv.zip | 260 lines