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Cell Type
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Tissue
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Disease
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Sex
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Technology
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Cell
893
Nucleus
659
Data Source
0
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Asap
43
Bgee
40
Cellxgene
2,077
Single cell portal
179
Sort
Most cells
Fewest cells
2339
datasets
Single Cell Portal
9,391 cells
Explore
Mus musculus
Mus musculus
Obsolete excitatory neuron
+2
Obsolete excitatory neuron
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Obsolete excitatory neuron
Brain microvascular endothelial cell
Obsolete inhibitory neuron
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
Related Links
Corresponding registered brain section (MD736) (section 112)
Corresponding registered brain section (MD736) (section 113)
Corresponding registered brain section (MD736) (section 115)
CELLxGENE
9,362 cells
•
Klughammer et al., 2024
A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+6
T cell
Chest wall
Chest wall
54-year-old stage
54-year-old stage
Breast cancer
Breast cancer
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
T cell
Cell of skeletal muscle
Malignant cell
Macrophage
Blood vessel smooth muscle cell
Blood vessel endothelial cell
Fibroblast
Tissue
Chest wall
Developmental stage
54-year-old stage
Disease
Breast cancer
Sex
Female
Technology
Slide-seqv2
Suspension type
Related Links
humantumoratlas.org
dbGaP Study:phs002371
CELLxGENE
9,354 cells
•
Gong et al., 2025
Multi-omic profiling reveals age-related immune dynamics in healthy adults
Explore
h5ad
Homo sapiens
Homo sapiens
Common myeloid progenitor
+4
Common myeloid progenitor
Blood
Blood
62-year-old stage
+50
62-year-old stage
Normal
+1
Normal
Female
+1
Female
10x gene expression flex
10x gene expression flex
Cell
Cell
Organism
Homo sapiens
Cell type
Common myeloid progenitor
Platelet
Erythrocyte
Basophil mast progenitor cell
Common lymphoid progenitor
Tissue
Blood
Developmental stage
62-year-old stage
43-year-old stage
66-year-old stage
54-year-old stage
49-year-old stage
42-year-old stage
59-year-old stage
64-year-old stage
46-year-old stage
56-year-old stage
68-year-old stage
55-year-old stage
88-year-old stage
86-year-old stage
82-year-old stage
57-year-old stage
83-year-old stage
60-year-old stage
75-year-old stage
80-year-old stage
77-year-old stage
74-year-old stage
63-year-old stage
76-year-old stage
61-year-old stage
48-year-old stage
89-year-old stage
78-year-old stage
72-year-old stage
67-year-old stage
80 year-old and over stage
47-year-old stage
81-year-old stage
79-year-old stage
52-year-old stage
44-year-old stage
87-year-old stage
58-year-old stage
84-year-old stage
65-year-old stage
85-year-old stage
50-year-old stage
45-year-old stage
53-year-old stage
69-year-old stage
73-year-old stage
51-year-old stage
70-year-old stage
40-year-old stage
41-year-old stage
71-year-old stage
Disease
Normal
Cytomegalovirus infection
Sex
Female
Male
Technology
10x gene expression flex
Suspension type
Cell
Related Links
apps.allenimmunology.org
GEO series:GSE275067
CELLxGENE collection:e9360edf-b0b7-4e01-bce8-e596814f13e7
CELLxGENE
9,337 cells
•
Szabo et al., 2021
Longitudinal profiling of respiratory and systemic immune responses reveals myeloid cell-driven lung inflammation in severe COVID-19
Explore
h5ad
Homo sapiens
Homo sapiens
Dendritic cell
+6
Dendritic cell
Blood
Blood
49-year-old stage
49-year-old stage
Covid-19
Covid-19
Male
Male
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Dendritic cell
B cell
Neutrophil
Platelet
Mature nk t cell
Plasma cell
Myeloid cell
Tissue
Blood
Developmental stage
49-year-old stage
Disease
Covid-19
Sex
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:simslab/cluster_diffex2018
COVID-19 cell atlas
Mendeley Data Dataset:fm7v43jrbk/2
CELLxGENE
9,286 cells
Explore
h5ad
Homo sapiens
Homo sapiens
Forebrain radial glial cell
+15
Forebrain radial glial cell
Brain meninx
+2
Brain meninx
Carnegie stage 21
+8
Carnegie stage 21
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Forebrain radial glial cell
Retinal ganglion cell
Glioblast (sensu vertebrata)
Neuroblast (sensu vertebrata)
Oligodendrocyte precursor cell
Neuron
Forebrain neuroblast
Spinal cord radial glial cell
Neuronal-restricted precursor
Retinal cell
Neural progenitor cell
Choroid plexus epithelial cell
Interneuron
Epithelial cell
Pinealocyte
Radial glial cell
Tissue
Brain meninx
Forebrain meninges
Meninx
Developmental stage
Carnegie stage 21
10th week post-fertilization stage
9th week post-fertilization stage
Carnegie stage 20
Carnegie stage 16
Carnegie stage 23
Carnegie stage 18
13th week post-fertilization stage
12th week post-fertilization stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:linnarsson-lab/human-meninges-development
CELLxGENE
9,275 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
Dn3 thymocyte
+5
Dn3 thymocyte
Thymus
Thymus
20-month-old stage and over
+2
20-month-old stage and over
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Mus musculus
Cell type
Dn3 thymocyte
Dn4 thymocyte
Double negative thymocyte
Immature t cell
Thymocyte
Professional antigen presenting cell
Tissue
Thymus
Developmental stage
20-month-old stage and over
18-month-old stage
3-month-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
GEO series:GSE132042
CZ BioHub Portal:tabula-muris-senis
protocols.io:smartseq2-for-htp-generation-of-facs-sorted-single-2uwgexe
Github:czbiohub/tabula-muris-senis
FigShare Dataset:Processed_files_to_use_with_scanpy_/8273102/2
CELLxGENE
9,263 cells
•
Fernandes Matuck et al., 2024
The Immunoregulatory Architecture of the Adult Oral Cavity
Explore
h5ad
Homo sapiens
Homo sapiens
Schwann cell
+17
Schwann cell
Hard palate
+1
Hard palate
32-year-old stage
+2
32-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Schwann cell
Natural killer cell
Dendritic cell
Melanocyte
B cell
Endothelial cell of lymphatic vessel
Neutrophil
Macrophage
Mural cell
Cd8-positive, alpha-beta t cell
Keratinocyte
Blood vessel endothelial cell
Fibroblast
Plasma cell
Langerhans cell
Mast cell
Cd4-positive helper t cell
Merkel cell
Tissue
Hard palate
Soft palate
Developmental stage
32-year-old stage
34-year-old stage
Seventh decade stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:Loci-lab/Oral-Craniofacial-Atlas
CELLxGENE
9,257 cells
•
Bakken et al., 2021
Comparative cellular analysis of motor cortex in human, marmoset and mouse
Explore
h5ad
Callithrix jacchus
Callithrix jacchus
Gabaergic neuron
Gabaergic neuron
Primary motor cortex
Primary motor cortex
Post-juvenile adult stage
Post-juvenile adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Callithrix jacchus
Cell type
Gabaergic neuron
Tissue
Primary motor cortex
Developmental stage
Post-juvenile adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
protocols.io:isolation-of-nuclei-from-adult-human-brain-tissue-j8nlk56k1l5r/v1
nemoanalytics.org
protocols.io:isolation-of-nuclei-from-adult-human-brain-tissue-eq2lyd1nqlx9/v2
Github:broadinstitute/Drop-seq
viewer.cytosplore.org
nemoanalytics.org
Github:AllenInstitute/BICCN_M1_Evo
Github:AllenInstitute/scrattch.hicat
NeMo archive:dat-ek5dbmu
protocols.io:extraction-of-nuclei-from-brain-tissue-2srged6
protocols.io:human-tissue-slicing-and-dissections-for-nuclear-i-dm6gpre85vzp
protocols.io:preparation-of-frozen-nuclei-for-single-nucleus-rn-eq2lyrdpgx9k/v1
CELLxGENE
9,249 cells
•
Bakken et al., 2021
Comparative cellular analysis of motor cortex in human, marmoset and mouse
Explore
h5ad
Mus musculus
Mus musculus
Gabaergic neuron
Gabaergic neuron
Primary motor cortex
Primary motor cortex
Prime adult stage
Prime adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Mus musculus
Cell type
Gabaergic neuron
Tissue
Primary motor cortex
Developmental stage
Prime adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
protocols.io:human-tissue-slicing-and-dissections-for-nuclear-i-dm6gpre85vzp
nemoanalytics.org
Github:broadinstitute/Drop-seq
viewer.cytosplore.org
nemoanalytics.org
Github:AllenInstitute/BICCN_M1_Evo
protocols.io:preparation-of-frozen-nuclei-for-single-nucleus-rn-eq2lyrdpgx9k/v1
Github:AllenInstitute/scrattch.hicat
NeMo archive:dat-ek5dbmu
protocols.io:isolation-of-nuclei-from-adult-human-brain-tissue-j8nlk56k1l5r/v1
protocols.io:isolation-of-nuclei-from-adult-human-brain-tissue-eq2lyd1nqlx9/v2
protocols.io:extraction-of-nuclei-from-brain-tissue-2srged6
CELLxGENE
9,203 cells
•
Gabitto et al., 2024
Integrated multimodal cell atlas of Alzheimer’s disease
Explore
h5ad
Homo sapiens
Homo sapiens
Caudal ganglionic eminence derived interneuron
Caudal ganglionic eminence derived interneuron
Middle temporal gyrus
Middle temporal gyrus
43-year-old stage
+23
43-year-old stage
Dementia
+1
Dementia
Female
+1
Female
10x multiome
+1
10x multiome
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Caudal ganglionic eminence derived interneuron
Tissue
Middle temporal gyrus
Developmental stage
43-year-old stage
68-year-old stage
88-year-old stage
86-year-old stage
82-year-old stage
83-year-old stage
60-year-old stage
75-year-old stage
80-year-old stage
77-year-old stage
Adult stage
89-year-old stage
78-year-old stage
72-year-old stage
80 year-old and over stage
81-year-old stage
87-year-old stage
84-year-old stage
65-year-old stage
85-year-old stage
50-year-old stage
29-year-old stage
69-year-old stage
70-year-old stage
Disease
Dementia
Normal
Sex
Female
Male
Technology
10x multiome
10x 3' v3
Suspension type
Nucleus
Related Links
Alzheimer's Disease Research Center
Adult Changes in Thought Study
BRaIN-lab
AD knowledge portal:syn26223298
AWS Open Data:allen-sea-ad-atlas
Allen Brain Map:seattle-alzheimers-disease
CELLxGENE
9,156 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Fibroblast
Fibroblast
Brodmann (1909) area 13
+87
Brodmann (1909) area 13
42-year-old stage
+3
42-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Fibroblast
Tissue
Brodmann (1909) area 13
Brodmann (1909) area 14
Brodmann (1909) area 19
Brodmann (1909) area 23
Brodmann (1909) area 24
Brodmann (1909) area 25
Brodmann (1909) area 32
Brodmann (1909) area 35
Brodmann (1909) area 38
Brodmann (1909) area 40
Brodmann (1909) area 43
Brodmann (1909) area 46
Accessory basal amygdaloid nucleus
Agranular insular cortex
Anterior cortical amygdaloid nucleus
Anterior nuclear group
Anterior olfactory nucleus
Basolateral amygdaloid nuclear complex
Bed nucleus of stria terminalis
Body of caudate nucleus
Central amygdaloid nucleus
Centromedian nucleus of thalamus
Cerebellar nuclear complex
Cerebellar vermis
Cerebrocerebellum
Claustrum of brain
Corticomedial nuclear complex
Cuneus cortex
Dentate gyrus of hippocampal formation
Dorsal tegmental nucleus
Epithalamus
Extrastriate cortex
Globus pallidus
Granular insular cortex
Gray matter of midbrain
Hippocampal field
Hypothalamus
Inferior frontal gyrus
Inferior olivary complex
Inferior temporal gyrus
Intralaminar nuclear group
Lateral amygdaloid nucleus
Lateral entorhinal cortex
Lateral geniculate body
Lateral nuclear group of thalamus
Lateral posterior nucleus of thalamus
Mammillary body
Medial dorsal nucleus of thalamus
Medial entorhinal cortex
Medial geniculate body
Medial zone of hypothalamus
Median tuberal portion
Midbrain nucleus
Midbrain tectum
Middle temporal gyrus
Nucleus accumbens
Nucleus of dorsal thalamus
Nucleus of medulla oblongata
Parabrachial nucleus
Perirhinal cortex
Piriform cortex
Pontine nuclear group
Pontine reticular formation
Pontine tegmentum
Posterior parahippocampal gyrus
Preoptic area
Pretectal region
Primary auditory cortex
Primary motor cortex
Primary somatosensory cortex
Primary visual cortex
Pulvinar nucleus
Putamen
Red nucleus
Retrosplenial region
Rostral ca3
Septal nuclear complex
Spinal cord
Subicular complex
Substantia innominata
Substantia nigra
Subthalamic nucleus
Superior parietal cortex
Superior temporal gyrus
Supraoptic nucleus
Temporal fusiform gyrus
Uncal ca1
Ventral anterior nucleus of thalamus
Developmental stage
42-year-old stage
60-year-old stage
50-year-old stage
29-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
NeMo archive:biccn/grant/u01_lein/linnarsson/transcriptome/sncell/10x_v3/human/raw
Github:linnarsson-lab/adult-human-brain
Github:linnarsson-lab/auto-annotation-ah
Single Cell Portal
9,149 cells
Explore
Mus musculus
Mus musculus
Endothelial cell of lymphatic vessel
Endothelial cell of lymphatic vessel
Normal
Normal
10x 3' v3
10x 3' v3
Organism
Mus musculus
Cell type
Endothelial cell of lymphatic vessel
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
Related Links
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