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896
Nucleus
659
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Asap
43
Bgee
40
Cellxgene
2,080
Single cell portal
183
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Most cells
Fewest cells
2346
datasets
CELLxGENE
16,743 cells
•
Jardine et al., 2021
Blood and immune development in human fetal bone marrow and Down syndrome
Explore
h5ad
Homo sapiens
Homo sapiens
Osteoblast
+31
Osteoblast
Bone marrow
Bone marrow
13th week post-fertilization stage
+2
13th week post-fertilization stage
Down syndrome
Down syndrome
Female
+1
Female
10x 5' v1
10x 5' v1
Cell
Cell
Organism
Homo sapiens
Cell type
Osteoblast
Neutrophil
Stromal cell
Natural killer cell
Erythrocyte
Endothelial cell
Mast cell
Cd8-positive, alpha-beta t cell
Plasmacytoid dendritic cell
Precursor b cell
Basophil mast progenitor cell
Primitive red blood cell
Macrophage
Regulatory t cell
Myelocyte
Immature innate lymphoid cell
Mature b cell
Promonocyte
Common myeloid progenitor
Cd14-positive monocyte
Hematopoietic multipotent progenitor cell
Eosinophil
Megakaryocyte
Progenitor cell
Promyelocyte
Mesenchymal stem cell
Immature b cell
Megakaryocyte-erythroid progenitor cell
Osteoclast
Dendritic cell
Cd16-negative, cd56-bright natural killer cell, human
Chondrocyte
Tissue
Bone marrow
Developmental stage
13th week post-fertilization stage
12th week post-fertilization stage
Fourth lmp month stage
Disease
Down syndrome
Sex
Female
Male
Technology
10x 5' v1
Suspension type
Cell
Related Links
fbm.cellatlas.io
haniffalab.com
Github:haniffalab/FCA_bone_marrow
ncbi.nlm.nih.gov
HumanCellAtlas:04ad400c-58cb-40a5-bc2b-2279e13a910b
ENA Project:PRJEB41514
ArrayExpress BioStudies:E-MTAB-9389
Single Cell Expression Atlas Experiment:E-CURD-112
Single Cell Expression Atlas Experiment:E-MTAB-9801
ArrayExpress BioStudies:E-MTAB-9801
ArrayExpress BioStudies:E-MTAB-10042
CELLxGENE
16,668 cells
•
Johansen et al., 2023
Interindividual variation in human cortical cell type abundance and expression
Explore
h5ad
Homo sapiens
Homo sapiens
L2/3-6 intratelencephalic projecting glutamatergic neuron
L2/3-6 intratelencephalic projecting glutamatergic neuron
Neocortex
Neocortex
Adult stage
Adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
L2/3-6 intratelencephalic projecting glutamatergic neuron
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
16,665 cells
•
Andrews et al., 2024
Single-cell, single-nucleus, and spatial transcriptomics characterization of the immunological landscape in the healthy and PSC human liver
Explore
h5ad
Homo sapiens
Homo sapiens
Natural killer cell
+7
Natural killer cell
Caudate lobe of liver
Caudate lobe of liver
Late adult stage
+2
Late adult stage
Normal
Normal
Female
+1
Female
10x 5' v1
+1
10x 5' v1
Cell
Cell
Organism
Homo sapiens
Cell type
Natural killer cell
Hepatic pit cell
Cd8-positive, alpha-beta t cell
Lymphocyte
Mature b cell
Myeloid cell
Cd4-positive, alpha-beta t cell
Erythroblast
Tissue
Caudate lobe of liver
Developmental stage
Late adult stage
Prime adult stage
Young adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' v1
10x 3' v2
Suspension type
Cell
Related Links
nature.com
GEO series:GSE240429
GEO series:GSE115469
GEO series:GSE243977
GEO series:GSE247128
GEO series:GSE245620
CELLxGENE
16,602 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Mammillary body neuron
Mammillary body neuron
Subthalamic nucleus
+10
Subthalamic nucleus
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
Mammillary body neuron
Tissue
Subthalamic nucleus
Medial geniculate body
Intralaminar nuclear group
Midbrain nucleus
Median tuberal portion
Dorsal tegmental nucleus
Substantia nigra
Hypothalamus
Primary motor cortex
Medial zone of hypothalamus
Mammillary body
Developmental stage
42-year-old stage
29-year-old stage
50-year-old stage
60-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
CELLxGENE
16,596 cells
•
Duran et al., 2025
A statistical framework for inferring genetic requirements from embryo-scale single-cell sequencing experiments
Explore
h5ad
Danio rerio
Danio rerio
Melanoblast
+4
Melanoblast
Multicellular anatomical structure
+1
Multicellular anatomical structure
Pharyngula:prim-15
+9
Pharyngula:prim-15
Normal
Normal
Sci-rna-seq3
Sci-rna-seq3
Nucleus
Nucleus
Organism
Danio rerio
Cell type
Melanoblast
Melanocyte
Xanthophore cell
Xanthoblast
Iridophore
Tissue
Multicellular anatomical structure
Neural crest
Developmental stage
Pharyngula:prim-15
Hatching:long-pec
Larval:protruding-mouth
Pharyngula:prim-25
Segmentation:26+ somites
Segmentation:14-19 somites
Hatching:pec-fin
Segmentation:20-25 somites
Pharyngula:high-pec
Pharyngula:prim-5
Disease
Normal
Sex
Technology
Sci-rna-seq3
Suspension type
Nucleus
Related Links
GEO series:GSE295164
cole-trapnelllab.github.io
DOI:10.1038/s41586-023-06720-2
ASAP
16,551 cells
•
Li et al., 2022
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly
Explore
h5ad
Drosophila melanogaster
Drosophila melanogaster
Indirect flight muscle cell
+1
Indirect flight muscle cell
Body wall
Body wall
Day 5 of adulthood
Day 5 of adulthood
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Organism
Drosophila melanogaster
Cell type
Indirect flight muscle cell
Hemocyte
Tissue
Body wall
Developmental stage
Day 5 of adulthood
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
CELLxGENE
16,540 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
Off-bipolar cell
+1
Off-bipolar cell
Retina
Retina
65-year-old stage
+3
65-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Off-bipolar cell
On-bipolar cell
Tissue
Retina
Developmental stage
65-year-old stage
77-year-old stage
70-year-old stage
79-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
GEO series:GSE135133
HumanCellAtlas:e090445c-6971-4212-bc5f-ae4ec3914102
BroadInstitute Single-Cell Portal:SCP484/nucseq-from-human-control-eyes-scrnaseq
CELLxGENE
16,475 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
Effector cd8-positive, alpha-beta t cell
+13
Effector cd8-positive, alpha-beta t cell
Pleural effusion
+5
Pleural effusion
69-year-old stage
+13
69-year-old stage
Small cell lung carcinoma
Small cell lung carcinoma
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Effector cd8-positive, alpha-beta t cell
Neutrophil
Natural killer cell
Gamma-delta t cell
Mast cell
Exhausted t cell
Plasmacytoid dendritic cell
Cd8-positive, alpha-beta memory t cell
Regulatory t cell
Plasma cell
Cd4-positive, alpha-beta t cell
B cell
Monocyte
Conventional dendritic cell
Tissue
Pleural effusion
Lung
Axilla
Liver
Adrenal gland
Lymph node
Developmental stage
69-year-old stage
75-year-old stage
71-year-old stage
68-year-old stage
55-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
47-year-old stage
Disease
Small cell lung carcinoma
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
data.humantumoratlas.org
dbGaP Study:phs002371
CELLxGENE
16,401 cells
•
Serizay et al., 2025
Cyclin switch tailors a cell cycle variant to orchestrate multiciliogenesis
Explore
h5ad
Mus musculus
Mus musculus
Oligodendrocyte precursor cell
+8
Oligodendrocyte precursor cell
Multiciliated ependymal cell
Multiciliated ependymal cell
Theiler stage 27
Theiler stage 27
Normal
Normal
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Oligodendrocyte precursor cell
Multiciliated ependymal cell
Oligodendrocyte
Microglial cell
Neural crest derived fibroblast
Deuterosomal cell
Neuroblast (sensu vertebrata)
Radial glial cell
Neuron associated cell
Tissue
Multiciliated ependymal cell
Developmental stage
Theiler stage 27
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
Cell
Related Links
DOI:10.1016/j.celrep.2024.115117
GEO series:GSE201773
DOI:10.5281/zenodo.14105247
Bgee
16,337 cells
•
Gray et al., 2022
A human breast atlas integrating single-cell proteomics and transcriptomics
Explore
scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens (tsv.gz)
scRNA-Seq droplet-based H5AD data per cell in Homo sapiens (h5ad)
Homo sapiens
Homo sapiens
T cell
+11
T cell
Thoracic mammary gland
Thoracic mammary gland
39-year-old stage
+2
39-year-old stage
Normal
Normal
Female
Female
10x genomics v2
10x genomics v2
Organism
Homo sapiens
Cell type
T cell
Natural killer cell
Endothelial cell of lymphatic vessel
Fibroblast of mammary gland
Contractile cell
Luminal epithelial cell of mammary gland
Lactocyte
Mammary microvascular endothelial cell
Basal-myoepithelial cell of mammary gland
Myeloid cell
Plasma cell
B cell
Tissue
Thoracic mammary gland
Developmental stage
39-year-old stage
41-year-old stage
36-year-old stage
Disease
Normal
Sex
Female
Technology
10x genomics v2
Suspension type
Related Links
SRA Project:SRP329970
CELLxGENE
16,319 cells
•
Johansen et al., 2023
Interindividual variation in human cortical cell type abundance and expression
Explore
h5ad
Homo sapiens
Homo sapiens
Astrocyte of the cerebral cortex
Astrocyte of the cerebral cortex
Neocortex
Neocortex
Adult stage
Adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Astrocyte of the cerebral cortex
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
Single Cell Portal
16,291 cells
Explore
Mus musculus
Mus musculus
Neutrophil
+11
Neutrophil
Encephalitis
Encephalitis
10x 3' v3
10x 3' v3
Organism
Mus musculus
Cell type
Neutrophil
Blood vessel endothelial cell
Natural killer cell
Gamma-delta t cell
Choroid plexus macrophage
Choroid plexus epithelial cell
Pericyte
Cd8-positive, alpha-beta regulatory t cell
Monocyte
Fibroblast of choroid plexus
Myofibroblast cell
Dendritic cell
Tissue
Developmental stage
Disease
Encephalitis
Sex
Technology
10x 3' v3
Suspension type
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