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Disease
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Technology
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Cell
896
Nucleus
659
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Asap
43
Bgee
40
Cellxgene
2,080
Single cell portal
183
Sort
Most cells
Fewest cells
2346
datasets
CELLxGENE
10,654 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Hippocampal ca4 neuron
Hippocampal ca4 neuron
Rostral ca3
+9
Rostral ca3
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
Hippocampal ca4 neuron
Tissue
Rostral ca3
Hippocampal field
Septal nuclear complex
Substantia nigra
Pulvinar nucleus
Primary motor cortex
Retrosplenial region
Dentate gyrus of hippocampal formation
Uncal ca1
Bed nucleus of stria terminalis
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
10,623 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
+5
T cell
Axilla
Axilla
37-year-old stage
37-year-old stage
Breast cancer
Breast cancer
Female
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
T cell
Blood vessel endothelial cell
Blood vessel smooth muscle cell
Macrophage
Malignant cell
Fibroblast
Tissue
Axilla
Developmental stage
37-year-old stage
Disease
Breast cancer
Sex
Female
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
humantumoratlas.org
dbGaP Study:phs002371
CELLxGENE
10,536 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
Nonkeratinized cell of epidermis
+3
Nonkeratinized cell of epidermis
Ectoderm-derived structure
+3
Ectoderm-derived structure
Pharyngula:prim-15
+9
Pharyngula:prim-15
Normal
Normal
Sci-rna-seq3
Sci-rna-seq3
Nucleus
Nucleus
Organism
Danio rerio
Cell type
Nonkeratinized cell of epidermis
Ionocyte
Goblet cell
Epidermal mucus secreting cell
Tissue
Ectoderm-derived structure
Multicellular anatomical structure
Integument
Taste bud
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
cole-trapnelllab.github.io
DOI:10.1038/s41586-023-06720-2
GEO series:GSE295164
CELLxGENE
10,533 cells
•
Mimpen et al., 2024
Single nucleus and spatial transcriptomic profiling of healthy human hamstring tendon
Explore
h5ad
Homo sapiens
Homo sapiens
Fast muscle cell
+10
Fast muscle cell
Tendon of semitendinosus
Tendon of semitendinosus
37-year-old stage
+3
37-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Fast muscle cell
Endothelial cell of lymphatic vessel
Slow muscle cell
Leukocyte
Skeletal muscle satellite cell
Neural cell
Endothelial cell of vascular tree
Adipocyte
Mural cell
Fibroblast
Skeletal muscle fiber
Tissue
Tendon of semitendinosus
Developmental stage
37-year-old stage
26-year-old stage
24-year-old stage
18-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
Github:Botnar-MSK-Atlas/hamstring_atlas
HumanCellAtlas:838d4660-3d62-4b08-b32d-dc5cbd93919d
CELLxGENE
10,459 cells
•
Suo et al., 2022
Mapping the developing human immune system across organs
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+6
T cell
Thymus
Thymus
Normal
Normal
10x 5' v1
10x 5' v1
Cell
Cell
Organism
Homo sapiens
Cell type
T cell
Natural killer cell
Erythrocyte
Mast cell
Double-positive, alpha-beta thymocyte
Group 3 innate lymphoid cell
Thymocyte
Tissue
Thymus
Developmental stage
Disease
Normal
Sex
Technology
10x 5' v1
Suspension type
Cell
Related Links
Human Cell Atlas Developmental:fetal-immune
Teichmann lab
UCSC Cell Browser:fetal-immune
Github:Teichlab/Pan_fetal_immune
DOI:10.1016/j.stem.2018.12.011
HumanCellAtlas:fcaa53cd-ba57-4bfe-af9c-eaa958f95c1a
ArrayExpress BioStudies:E-MTAB-11341
ArrayExpress BioStudies:E-MTAB-11343
BroadInstitute Single-Cell Portal:SCP1843
CELLxGENE
10,419 cells
•
Marshall et al., 2022
High-resolution Slide-seqV2 spatial transcriptomics enables discovery of disease-specific cell neighborhoods and pathways
Explore
h5ad
Homo sapiens
Homo sapiens
Podocyte
+15
Podocyte
Cortex of kidney
Cortex of kidney
75-year-old stage
75-year-old stage
Normal
Normal
Male
Male
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
Podocyte
Parietal epithelial cell
Endothelial cell
Kidney loop of henle thin descending limb epithelial cell
Kidney interstitial fibroblast
Blood vessel smooth muscle cell
Kidney collecting duct intercalated cell
Leukocyte
Kidney distal convoluted tubule epithelial cell
Kidney collecting duct principal cell
Kidney connecting tubule epithelial cell
Kidney loop of henle thick ascending limb epithelial cell
Kidney loop of henle epithelial cell
Mesangial cell
Pericyte
Kidney proximal convoluted tubule epithelial cell
Tissue
Cortex of kidney
Developmental stage
75-year-old stage
Disease
Normal
Sex
Male
Technology
Slide-seqv2
Suspension type
Related Links
Github:marshalljamie/Kidney-Slide-seq
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
Github:MacoskoLab/slideseq-tools
grekalab.org
GEO series:GSE190094
CELLxGENE
10,411 cells
•
Garcia-Alonso et al., 2022
Single-cell roadmap of human gonadal development
Explore
h5ad
Mus musculus
Mus musculus
Female germ cell
+4
Female germ cell
Testis
+5
Testis
Theiler stage 22
+8
Theiler stage 22
Normal
Normal
Female
+1
Female
10x 5' v1
+2
10x 5' v1
Cell
Cell
Organism
Mus musculus
Cell type
Female germ cell
Oogonial cell
Oocyte
Male germ cell
Primordial germ cell
Tissue
Testis
Mesonephros
Ovary
Gonad primordium
Mesoderm
Gonad
Developmental stage
Theiler stage 22
Theiler stage 27
Theiler stage 24
5-day-old stage
Theiler stage 17
Theiler stage 19
Theiler stage 26
Theiler stage 20
Theiler stage 21
Disease
Normal
Sex
Female
Male
Technology
10x 5' v1
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
ArrayExpress BioStudies:E-MTAB-10551
ArrayExpress BioStudies:E-MTAB-11480
reproductivecellatlas.org
ventolab.org
CELLxGENE
10,377 cells
•
Lim et al., 2025
A non-canonical lymphoblast in refractory childhood T-cell leukaemia
Explore
h5ad
Homo sapiens
Homo sapiens
Malignant cell
Malignant cell
Bone marrow
Bone marrow
Pediatric stage
Pediatric stage
T-cell childhood acute lymphocytic leukemia
T-cell childhood acute lymphocytic leukemia
Male
Male
10x 5' v2
10x 5' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Malignant cell
Tissue
Bone marrow
Developmental stage
Pediatric stage
Disease
T-cell childhood acute lymphocytic leukemia
Sex
Male
Technology
10x 5' v2
Suspension type
Cell
Related Links
EGA dataset:EGAD00001009058
EGA dataset:EGAD50000001128
EGA dataset:EGAD00001015727
EGA dataset:EGAD00001015673
dbgap.ncbi.nlm.nih.gov
Github:BehjatiLab/TALL_refractory
synapse.org:Synapse:syn54032669/wiki/627818
CELLxGENE
10,363 cells
•
Maatz et al., 2025
The cellular and molecular cardiac tissue responses in human inflammatory cardiomyopathies after SARS-CoV-2 infection and COVID-19 vaccination
Explore
h5ad
Homo sapiens
Homo sapiens
Cd141-positive myeloid dendritic cell
+4
Cd141-positive myeloid dendritic cell
Apex of heart
+1
Apex of heart
21-year-old stage
+22
21-year-old stage
Myocarditis
+1
Myocarditis
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Cd141-positive myeloid dendritic cell
Cycling macrophage
Macrophage
Myeloid cell
Monocyte
Tissue
Apex of heart
Heart left ventricle
Developmental stage
21-year-old stage
26-year-old stage
Sixth decade stage
61-year-old stage
52-year-old stage
30-year-old stage
29-year-old stage
38-year-old stage
Fifth decade stage
55-year-old stage
28-year-old stage
Third decade stage
49-year-old stage
24-year-old stage
Seventh decade stage
25-year-old stage
32-year-old stage
64-year-old stage
70-year-old stage
31-year-old stage
19-year-old stage
Eighth decade stage
27-year-old stage
Disease
Myocarditis
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Nucleus
Related Links
EGA Study:EGAS50000000769
EGA dataset:EGAD00001009292
DOI:10.1126/science.abo1984
DOI:10.1038/s41586-020-2797-4
ENA Project:PRJEB39602
CELLxGENE
10,268 cells
•
Tran et al., 2021
Single-nucleus transcriptome analysis reveals cell-type-specific molecular signatures across reward circuitry in the human brain
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+8
T cell
Hippocampal formation
Hippocampal formation
54-year-old stage
+2
54-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
T cell
Glutamatergic neuron
Oligodendrocyte precursor cell
Oligodendrocyte
Microglial cell
Gabaergic interneuron
Mural cell
Pvalb gabaergic interneuron
Astrocyte
Tissue
Hippocampal formation
Developmental stage
54-year-old stage
51-year-old stage
40-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
research.libd.org
Github:LieberInstitute/10xPilot_snRNAseq-human
CELLxGENE
10,250 cells
•
Marshall et al., 2022
High-resolution Slide-seqV2 spatial transcriptomics enables discovery of disease-specific cell neighborhoods and pathways
Explore
h5ad
Mus musculus
Mus musculus
Podocyte
+11
Podocyte
Kidney
Kidney
13-week-old stage
13-week-old stage
Diabetic kidney disease
Diabetic kidney disease
Male
Male
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Podocyte
Endothelial cell
Kidney interstitial fibroblast
Blood vessel smooth muscle cell
Kidney collecting duct intercalated cell
Leukocyte
Macrophage
Kidney distal convoluted tubule epithelial cell
Kidney collecting duct principal cell
Kidney loop of henle thick ascending limb epithelial cell
Mesangial cell
Kidney proximal convoluted tubule epithelial cell
Tissue
Kidney
Developmental stage
13-week-old stage
Disease
Diabetic kidney disease
Sex
Male
Technology
Slide-seqv2
Suspension type
Related Links
GEO series:GSE190094
Github:marshalljamie/Kidney-Slide-seq
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
Github:MacoskoLab/slideseq-tools
grekalab.org
CELLxGENE
10,224 cells
•
Redman et al., 2024
Cell Culture Differentiation and Proliferation Conditions Influence the <i>In Vitro<i> Regeneration of the Human Airway Epithelium
Explore
h5ad
Homo sapiens
Homo sapiens
Lung secretory cell
+7
Lung secretory cell
Epithelial cell of lung
Epithelial cell of lung
34-year-old stage
+1
34-year-old stage
Normal
Normal
Male
Male
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Lung secretory cell
Bronchial goblet cell
Deuterosomal cell
Squamous epithelial cell
Respiratory tract suprabasal cell
Epithelial cell of lung
Multiciliated epithelial cell
Basal cell of epithelium of bronchus
Tissue
Epithelial cell of lung
Developmental stage
34-year-old stage
62-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
GEO series:GSE243045
EGA dataset:EGAD00001011362
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