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Cell Type
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Tissue
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Developmental Stage
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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
CELLxGENE
8,193 cells
•
Orozco et al., 2020
Integration of eQTL and a Single-Cell Atlas in the Human Eye Identifies Causal Genes for Age-Related Macular Degeneration
Explore
h5ad
Homo sapiens
Homo sapiens
Schwann cell
+9
Schwann cell
Retina
Retina
77-year-old stage
+3
77-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Schwann cell
Astrocyte
Melanocyte
T cell
B cell
Pericyte
Retinal pigment epithelial cell
Mueller cell
Endothelial cell
Myeloid cell
Tissue
Retina
Developmental stage
77-year-old stage
79-year-old stage
65-year-old stage
70-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
HumanCellAtlas:e090445c-6971-4212-bc5f-ae4ec3914102
GEO series:GSE135133
BroadInstitute Single-Cell Portal:SCP484/nucseq-from-human-control-eyes-scrnaseq
Single Cell Portal
8,190 cells
Explore
Mus musculus
Mus musculus
Oligodendrocyte
+3
Oligodendrocyte
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Oligodendrocyte
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 (MD716) (section 40)
Corresponding registered brain section (MD716) (section 41)
Corresponding registered brain section (MD716) (section 42)
Corresponding registered brain section (MD716) (section 43)
Corresponding registered brain section (MD716) (section 44)
Corresponding registered brain section (MD716) (section 45)
CELLxGENE
8,172 cells
•
de Morree et al., 2025
A molecular cell atlas of mouse lemur, an emerging model primate
Explore
h5ad
Microcebus murinus
Microcebus murinus
Plasmacytoid dendritic cell
+33
Plasmacytoid dendritic cell
Pancreas
Pancreas
Post-juvenile adult stage
Post-juvenile adult stage
Normal
Normal
Female
+1
Female
10x 3' v2
+1
10x 3' v2
Cell
Cell
Organism
Microcebus murinus
Cell type
Plasmacytoid dendritic cell
Natural killer cell
Dendritic cell
Pancreatic d cell
Pancreatic endocrine cell
T cell
B cell
Endothelial cell of artery
Pericyte
Reticular cell
Conventional dendritic cell
Endothelial cell of lymphatic vessel
Neutrophil
Lymphocyte
Pancreatic acinar cell
Non-myelinating schwann cell
Type b pancreatic cell
Monocyte
Mature nk t cell
Cd4-positive, alpha-beta t cell
Macrophage
Cd8-positive, alpha-beta t cell
Vascular associated smooth muscle cell
Adipocyte
Stromal cell
Capillary endothelial cell
Pancreatic pp cell
Pancreatic ductal cell
Vein endothelial cell
Epithelial cell of exocrine pancreas
Fibroblast
Plasma cell
Pancreatic a cell
Mesothelial cell
Tissue
Pancreas
Developmental stage
Post-juvenile adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Smart-seq2
Suspension type
Cell
Related Links
tabula-microcebus.sf.czbiohub.org
app.globus.org
UCSC Cell Browser:tabula-microcebus
CELLxGENE
8,168 cells
•
Leng et al., 2021
Molecular characterization of selectively vulnerable neurons in Alzheimer’s disease
Explore
h5ad
Homo sapiens
Homo sapiens
Oligodendrocyte
Oligodendrocyte
Entorhinal cortex
Entorhinal cortex
82-year-old stage
+7
82-year-old stage
Alzheimer disease
+1
Alzheimer disease
Male
Male
10x 3' v2
10x 3' v2
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Oligodendrocyte
Tissue
Entorhinal cortex
Developmental stage
82-year-old stage
60-year-old stage
77-year-old stage
72-year-old stage
80 year-old and over stage
87-year-old stage
50-year-old stage
71-year-old stage
Disease
Alzheimer disease
Normal
Sex
Male
Technology
10x 3' v2
Suspension type
Nucleus
Related Links
GEO series:GSE147528
kampmannlab.ucsf.edu
HumanCellAtlas:7dcffc32-7c82-4396-9a4f-88b5579bfe8a
synapse.org:#!Synapse:syn21788402/wiki/601825
CELLxGENE
8,166 cells
•
Bakken et al., 2021
Comparative cellular analysis of motor cortex in human, marmoset and mouse
Explore
h5ad
Callithrix jacchus
Callithrix jacchus
Glutamatergic neuron
Glutamatergic 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
Glutamatergic 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
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-eq2lyd1nqlx9/v2
protocols.io:extraction-of-nuclei-from-brain-tissue-2srged6
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
Cerebellum
+26
Cerebellum
10th week post-fertilization stage
+11
10th week post-fertilization stage
Normal
Normal
10x 3' v2
+1
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Macrophage
Tissue
Cerebellum
Hippocampal formation
Entorhinal cortex
Brain
Caudate-putamen
Upper layers of the cortex
Hindbrain
Midbrain
Pons
Forebrain
Frontal cortex
Head
Lower layers of the cortex
Hypothalamus
Dorsal plus ventral thalamus
Striatum
Telencephalon
Metencephalon
Basal forebrain
Diencephalon
Midbrain tectum
Cerebral subcortex
Medulla oblongata
Occipital cortex
Cortex
Choroid plexus epithelium
Cerebellar peduncular complex
Developmental stage
10th week post-fertilization stage
14th week post-fertilization stage
9th week post-fertilization stage
11th week post-fertilization stage
Carnegie stage 15
Carnegie stage 20
Carnegie stage 16
15th week post-fertilization stage
Carnegie stage 22
Carnegie stage 18
13th week post-fertilization stage
12th week post-fertilization stage
Disease
Normal
Sex
Technology
10x 3' v2
10x 3' v3
Suspension type
Cell
Related Links
EGA dataset:EGAD00001006049
Github:linnarsson-lab/developing-human-brain?tab=readme-ov-file
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
NeMo archive:dat-p3eei0g
Github:AllenInstitute/human_variation
Allen Brain Map:classes/multimodal-characterization
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
Hepatocyte
+7
Hepatocyte
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
Hepatocyte
T cell
Monocyte
Malignant cell
Mature nk t cell
Macrophage
Endothelial cell
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
Oligodendrocyte
+21
Oligodendrocyte
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
Oligodendrocyte
Astrocyte
Hippocampal ca4 neuron
T cell
Medial ganglionic eminence derived interneuron
Pvalb chandelier gabaergic interneuron
Microglial cell
Oligodendrocyte precursor cell
Neuron
Ependymal cell
Pericyte
Committed oligodendrocyte precursor
Vascular associated smooth muscle cell
Sst chodl gabaergic interneuron
Hippocampal ca1-3 neuron
Endothelial cell
Amygdala excitatory neuron
Caudal ganglionic eminence derived interneuron
Dentate gyrus granule cell
Central nervous system macrophage
Fibroblast
Lamp5 lhx6 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
Red nucleus
+15
Red nucleus
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
Red nucleus
Dorsal tegmental nucleus
Parabrachial nucleus
Inferior olivary complex
Globus pallidus
Cerebellar nuclear complex
Pontine tegmentum
Cerebellar vermis
Pulvinar nucleus
Midbrain tectum
Cerebrocerebellum
Pontine reticular formation
Nucleus of medulla oblongata
Mammillary body
Spinal cord
Septal nuclear complex
Developmental stage
42-year-old stage
50-year-old stage
29-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
8,030 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
Lung
+7
Lung
62-year-old stage
+24
62-year-old stage
Small cell lung carcinoma
+2
Small cell lung carcinoma
Female
+1
Female
10x 3' v2
+2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Erythrocyte
Endothelial cell
Fibroblast
Tissue
Lung
Adrenal gland
Brain
Pleural effusion
Liver
Lymph node
Axilla
Bone spine
Developmental stage
62-year-old stage
64-year-old stage
68-year-old stage
55-year-old stage
82-year-old stage
57-year-old stage
75-year-old stage
80-year-old stage
77-year-old stage
74-year-old stage
76-year-old stage
78-year-old stage
72-year-old stage
67-year-old stage
47-year-old stage
81-year-old stage
79-year-old stage
44-year-old stage
84-year-old stage
65-year-old stage
85-year-old stage
69-year-old stage
73-year-old stage
70-year-old stage
71-year-old stage
Disease
Small cell lung carcinoma
Lung adenocarcinoma
Normal
Sex
Female
Male
Technology
10x 3' v2
10x 3' transcription profiling
10x 3' v3
Suspension type
Cell
Related Links
data.humantumoratlas.org
dbGaP Study:phs002371
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