• v2 A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

Summary

Metadata

Dataset Type

Integrated. The file includes an integrated collection of datasets.

Total Cells

107,502

organism

Mus musculus

disease

normal

assay

10x 3' v2 (53,751 cells)10x 3' v3 (53,751 cells)

tissue

olfactory cortex (101,347 cells)striatum (4,493 cells)neocortex (785 cells)cerebral cortex (438 cells)hippocampal formation (231 cells)pallidum (199 cells)dorsal plus ventral thalamus (4 cells)midbrain (2 cells)hypothalamus (2 cells)pons (1 cells)

Cell Labels

class

Description

The top level of cell type definition in the mouse whole brain taxonomy. It is primarily determined by broad brain region and neurotransmitter type. All cells within a subclass belong to the same class. Class provides a broader categorization of cell types.

Annotation Method

manual

Cell Labels (1)

Cells (107,502)

05 OB-IMN GABA

107,502

subclass

Description

The coarse level of cell type definition in the mouse whole brain taxonomy. All cells within a supertype belong to the same subclass. Subclass groups together related supertypes.

Annotation Method

manual

Cell Labels (7)

Cells (107,502)

041 OB-in Frmd7 Gaba

79,816

045 OB-STR-CTX Inh IMN

10,746

042 OB-out Frmd7 Gaba

5,997

044 OB Dopa-Gaba

4,662

040 OB Trdn Gaba

3,507

039 OB Meis2 Thsd7b Gaba

2,163

043 OB-mi Frmd7 Gaba

611

supertype

Description

The second finest level of cell type definition in the mouse whole brain taxonomy. All cells within a cluster belong to the same supertype. Supertype groups together similar clusters.

Annotation Method

manual

Cell Labels (30)

Cells (107,502)

0150 OB-in Frmd7 Gaba_1

38,299

0151 OB-in Frmd7 Gaba_2

34,048

0158 OB-out Frmd7 Gaba_1

5,366

0169 OB-STR-CTX Inh IMN_4

4,384

0162 OB Dopa-Gaba_1

4,296

0167 OB-STR-CTX Inh IMN_2

3,459

0149 OB Trdn Gaba_2

2,511

0154 OB-in Frmd7 Gaba_5

2,172

0152 OB-in Frmd7 Gaba_3

2,063

0153 OB-in Frmd7 Gaba_4

1,876

0166 OB-STR-CTX Inh IMN_1

1,628

0148 OB Trdn Gaba_1

996

cluster

Description

The finest level of cell type definition in the mouse whole brain taxonomy. Cells within a cluster share similar characteristics and belong to the same supertype.

Annotation Method

manual

Cell Labels (105)

Cells (107,502)

0537 OB-in Frmd7 Gaba_1

12,411

0548 OB-in Frmd7 Gaba_2

8,143

0540 OB-in Frmd7 Gaba_1

8,074

0542 OB-in Frmd7 Gaba_2

6,223

0543 OB-in Frmd7 Gaba_2

4,720

0545 OB-in Frmd7 Gaba_2

4,599

0533 OB-in Frmd7 Gaba_1

4,266

0544 OB-in Frmd7 Gaba_2

4,229

0612 OB-STR-CTX Inh IMN_4

3,464

0547 OB-in Frmd7 Gaba_2

3,129

0538 OB-in Frmd7 Gaba_1

3,106

0539 OB-in Frmd7 Gaba_1

2,657