Home
Data
Contribute
Stats
Resources
Metadata schema
Tools
Community
About
Contact us
Organism
0
Clear
Cell Type
0
Clear
Tissue
0
Clear
Developmental Stage
0
Clear
Disease
0
Clear
Sex
0
Clear
Technology
0
Clear
Suspension Type
0
Clear
Cell
896
Nucleus
659
Data Source
0
Clear
Asap
43
Bgee
40
Cellxgene
2,080
Single cell portal
183
Sort
Most cells
Fewest cells
2346
datasets
CELLxGENE
8,156 cells
•
Chen et al., 2025
Determinants of sensitivity to HER2-targeted antibody drug conjugates in urothelial cancer
Explore
h5ad
Homo sapiens
Homo sapiens
Neoplastic cell
Neoplastic cell
Urinary bladder
Urinary bladder
Adult stage
Adult stage
Urinary bladder cancer
Urinary bladder cancer
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Neoplastic cell
Tissue
Urinary bladder
Developmental stage
Adult stage
Disease
Urinary bladder cancer
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
CELLxGENE
8,102 cells
•
Braun et al., 2023
Comprehensive cell atlas of the first-trimester developing human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Macrophage
Macrophage
Choroid plexus epithelium
+26
Choroid plexus epithelium
13th week post-fertilization stage
+11
13th week post-fertilization stage
Normal
Normal
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Macrophage
Tissue
Choroid plexus epithelium
Striatum
Medulla oblongata
Hindbrain
Telencephalon
Cortex
Midbrain
Dorsal plus ventral thalamus
Lower layers of the cortex
Frontal cortex
Entorhinal cortex
Midbrain tectum
Metencephalon
Basal forebrain
Cerebellum
Brain
Hypothalamus
Cerebellar peduncular complex
Upper layers of the cortex
Caudate-putamen
Hippocampal formation
Diencephalon
Pons
Cerebral subcortex
Occipital cortex
Forebrain
Head
Developmental stage
13th week post-fertilization stage
14th week post-fertilization stage
15th week post-fertilization stage
12th week post-fertilization stage
Carnegie stage 20
9th week post-fertilization stage
10th week post-fertilization stage
Carnegie stage 22
Carnegie stage 16
Carnegie stage 15
Carnegie stage 18
11th week post-fertilization stage
Disease
Normal
Sex
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
Github:linnarsson-lab/developing-human-brain?tab=readme-ov-file
EGA dataset:EGAD00001006049
CELLxGENE
8,093 cells
•
Johansen et al., 2023
Interindividual variation in human cortical cell type abundance and expression
Explore
h5ad
Homo sapiens
Homo sapiens
Lamp5 gabaergic interneuron
Lamp5 gabaergic interneuron
Neocortex
Neocortex
Adult stage
Adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Lamp5 gabaergic interneuron
Tissue
Neocortex
Developmental stage
Adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
knowledge.brain-map.org
Allen Brain Map Atlases:rnaseq/human-mtg-10x_sea-ad
Allen Brain Map:classes/multimodal-characterization
NeMo archive:dat-p3eei0g
Github:AllenInstitute/human_variation
CELLxGENE
8,086 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
+7
T cell
Liver
Liver
41-year-old stage
41-year-old stage
Breast cancer
Breast cancer
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
T cell
Hepatocyte
Endothelial cell
Mature nk t cell
Macrophage
Malignant cell
Monocyte
Fibroblast
Tissue
Liver
Developmental stage
41-year-old stage
Disease
Breast cancer
Sex
Female
Technology
Slide-seqv2
Suspension type
Related Links
humantumoratlas.org
dbGaP Study:phs002371
CELLxGENE
8,077 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+21
T cell
Rostral ca3
Rostral ca3
50-year-old stage
50-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
T cell
Central nervous system macrophage
Oligodendrocyte precursor cell
Endothelial cell
Oligodendrocyte
Amygdala excitatory neuron
Committed oligodendrocyte precursor
Dentate gyrus granule cell
Hippocampal ca1-3 neuron
Lamp5 lhx6 neuron
Pvalb chandelier gabaergic interneuron
Medial ganglionic eminence derived interneuron
Ependymal cell
Microglial cell
Pericyte
Neuron
Caudal ganglionic eminence derived interneuron
Vascular associated smooth muscle cell
Sst chodl gabaergic interneuron
Astrocyte
Fibroblast
Hippocampal ca4 neuron
Tissue
Rostral ca3
Developmental stage
50-year-old stage
Disease
Normal
Sex
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
CELLxGENE
8,041 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Bergmann glial cell
Bergmann glial cell
Pontine reticular formation
+15
Pontine reticular formation
42-year-old stage
+2
42-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Bergmann glial cell
Tissue
Pontine reticular formation
Parabrachial nucleus
Nucleus of medulla oblongata
Red nucleus
Pontine tegmentum
Globus pallidus
Septal nuclear complex
Cerebellar nuclear complex
Dorsal tegmental nucleus
Midbrain tectum
Inferior olivary complex
Cerebrocerebellum
Pulvinar nucleus
Cerebellar vermis
Spinal cord
Mammillary body
Developmental stage
42-year-old stage
29-year-old stage
50-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
Github:linnarsson-lab/adult-human-brain
Github:linnarsson-lab/auto-annotation-ah
NeMo archive:biccn/grant/u01_lein/linnarsson/transcriptome/sncell/10x_v3/human/raw
CELLxGENE
8,030 cells
•
Chan et al., 2021
Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer
Explore
h5ad
Homo sapiens
Homo sapiens
Erythrocyte
+2
Erythrocyte
Pleural effusion
+7
Pleural effusion
69-year-old stage
+24
69-year-old stage
Lung adenocarcinoma
+2
Lung adenocarcinoma
Female
+1
Female
10x 3' transcription profiling
+2
10x 3' transcription profiling
Cell
Cell
Organism
Homo sapiens
Cell type
Erythrocyte
Endothelial cell
Fibroblast
Tissue
Pleural effusion
Lung
Axilla
Liver
Bone spine
Brain
Adrenal gland
Lymph node
Developmental stage
69-year-old stage
75-year-old stage
65-year-old stage
71-year-old stage
85-year-old stage
68-year-old stage
44-year-old stage
55-year-old stage
84-year-old stage
82-year-old stage
80-year-old stage
57-year-old stage
72-year-old stage
81-year-old stage
74-year-old stage
67-year-old stage
77-year-old stage
64-year-old stage
62-year-old stage
70-year-old stage
78-year-old stage
47-year-old stage
76-year-old stage
79-year-old stage
73-year-old stage
Disease
Lung adenocarcinoma
Normal
Small cell lung carcinoma
Sex
Female
Male
Technology
10x 3' transcription profiling
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
data.humantumoratlas.org
dbGaP Study:phs002371
CELLxGENE
7,999 cells
•
Reichart et al., 2022
Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies
Explore
h5ad
Homo sapiens
Homo sapiens
Cardiac neuron
Cardiac neuron
Heart right ventricle
+3
Heart right ventricle
Pediatric stage
+7
Pediatric stage
Arrhythmogenic right ventricular cardiomyopathy
+3
Arrhythmogenic right ventricular cardiomyopathy
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Cardiac neuron
Tissue
Heart right ventricle
Apex of heart
Heart left ventricle
Interventricular septum
Developmental stage
Pediatric stage
Sixth decade stage
Fifth decade stage
Third decade stage
Seventh decade stage
Postnatal stage
Fourth decade stage
Eighth decade stage
Disease
Arrhythmogenic right ventricular cardiomyopathy
Dilated cardiomyopathy
Normal
Non-compaction cardiomyopathy
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Nucleus
Related Links
Github:heiniglab/DCM_heart_cell_atlas
Zenodo record:6962685#.YuyuihxBzKE
EGA Study:EGAS00001006374
CELLxGENE
7,976 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
Granulocyte
+11
Granulocyte
Trachea
Trachea
3-month-old stage
3-month-old stage
Normal
Normal
Male
Male
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Mus musculus
Cell type
Granulocyte
Endothelial cell
Neuroendocrine cell
Epithelial cell
Macrophage
Mesenchymal cell
Mesenchymal stem cell
Smooth muscle cell of trachea
Blood cell
Fibroblast
Basal epithelial cell of tracheobronchial tree
Chondrocyte
Tissue
Trachea
Developmental stage
3-month-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
GEO series:GSE132042
FigShare Dataset:Processed_files_to_use_with_scanpy_/8273102/2
CZ BioHub Portal:tabula-muris-senis
Github:czbiohub/tabula-muris-senis
protocols.io:smartseq2-for-htp-generation-of-facs-sorted-single-2uwgexe
CELLxGENE
7,846 cells
•
Sampath Kumar et al., 2023
Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis
Explore
h5ad
Mus musculus
Mus musculus
Cardiac valve cell
+15
Cardiac valve cell
Embryo
Embryo
Theiler stage 14
Theiler stage 14
Normal
Normal
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Cardiac valve cell
Spinal cord interneuron
Premigratory neural crest cell
Paraxial cell
Notochordal cell
Neuroplacodal cell
Neurectodermal cell
Hemangioblast
Mesodermal cell
Gut endothelial cell
Primitive red blood cell
Splanchnic mesodermal cell
Surface ectodermal cell
Midbrain dopaminergic neuron
Endodermal cell
Anterior visceral endoderm cell
Tissue
Embryo
Developmental stage
Theiler stage 14
Disease
Normal
Sex
Technology
Slide-seqv2
Suspension type
Related Links
Chen Lab
GEO series:GSE197353
figshare.com
FigShare Dataset:E8_5_Embryo2_h5ad/21695849/1
FigShare Dataset:E9_0_Embryo_h5ad/21695879/1
CELLxGENE
7,805 cells
•
Bakken et al., 2021
Comparative cellular analysis of motor cortex in human, marmoset and mouse
Explore
h5ad
Homo sapiens
Homo sapiens
Glutamatergic neuron
Glutamatergic neuron
Primary motor cortex
Primary motor cortex
50-year-old stage
+1
50-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Glutamatergic neuron
Tissue
Primary motor cortex
Developmental stage
50-year-old stage
60-year-old 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
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
protocols.io:extraction-of-nuclei-from-brain-tissue-2srged6
protocols.io:isolation-of-nuclei-from-adult-human-brain-tissue-eq2lyd1nqlx9/v2
NeMo archive:dat-ek5dbmu
CELLxGENE
7,803 cells
•
Stewart et al., 2019
Spatiotemporal immune zonation of the human kidney
Explore
h5ad
Homo sapiens
Homo sapiens
Neutrophil
+11
Neutrophil
Renal medulla
+4
Renal medulla
53-year-old stage
+11
53-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Neutrophil
Natural killer cell
Mature nk t cell
Mast cell
Cd8-positive, alpha-beta t cell
Kidney resident macrophage
Classical monocyte
Plasmacytoid dendritic cell
Cd4-positive, alpha-beta t cell
B cell
Dendritic cell
Non-classical monocyte
Tissue
Renal medulla
Renal pelvis
Kidney blood vessel
Kidney
Cortex of kidney
Developmental stage
53-year-old stage
2-year-old stage
44-year-old stage
12-year-old stage
72-year-old stage
49-year-old stage
67-year-old stage
64-year-old stage
19-month-old stage
70-year-old stage
63-year-old stage
4-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
kidneycellatlas.org
UCSC Cell Browser:kidney-atlas
UCSC Genome Browser:hgTrackUi?db=hg38&g=kidneyStewart&position=default
Single Cell Expression Atlas Experiment:E-HCAD-10
HumanCellAtlas:abe1a013-af7a-45ed-8c26-f3793c24a1f4
1
2
…
130
131
132
133
134
…
390
391
Close