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Tissue
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Disease
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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
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Most cells
Fewest cells
2339
datasets
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:EGAD00001015727
EGA dataset:EGAD00001015673
dbgap.ncbi.nlm.nih.gov
synapse.org:Synapse:syn54032669/wiki/627818
Github:BehjatiLab/TALL_refractory
EGA dataset:EGAD00001009058
EGA dataset:EGAD50000001128
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
Monocyte
+4
Monocyte
Heart left ventricle
+1
Heart left ventricle
38-year-old stage
+22
38-year-old stage
Myocarditis
+1
Myocarditis
Female
+1
Female
10x 3' v2
+1
10x 3' v2
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Monocyte
Cycling macrophage
Macrophage
Cd141-positive myeloid dendritic cell
Myeloid cell
Tissue
Heart left ventricle
Apex of heart
Developmental stage
38-year-old stage
32-year-old stage
31-year-old stage
49-year-old stage
21-year-old stage
30-year-old stage
19-year-old stage
64-year-old stage
25-year-old stage
Seventh decade stage
24-year-old stage
55-year-old stage
28-year-old stage
Fifth decade stage
61-year-old stage
26-year-old stage
27-year-old stage
Sixth decade stage
52-year-old stage
Eighth decade stage
Third decade stage
29-year-old stage
70-year-old stage
Disease
Myocarditis
Normal
Sex
Female
Male
Technology
10x 3' v2
10x 3' v3
Suspension type
Nucleus
Related Links
EGA Study:EGAS50000000769
ENA Project:PRJEB39602
EGA dataset:EGAD00001009292
DOI:10.1126/science.abo1984
DOI:10.1038/s41586-020-2797-4
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
Oligodendrocyte
+8
Oligodendrocyte
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
Oligodendrocyte
Astrocyte
T cell
Microglial cell
Oligodendrocyte precursor cell
Mural cell
Pvalb gabaergic interneuron
Gabaergic interneuron
Glutamatergic neuron
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
Kidney loop of henle thick ascending limb epithelial cell
+11
Kidney loop of henle thick ascending limb epithelial cell
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
Kidney loop of henle thick ascending limb epithelial cell
Kidney interstitial fibroblast
Leukocyte
Kidney proximal convoluted tubule epithelial cell
Podocyte
Kidney collecting duct principal cell
Macrophage
Blood vessel smooth muscle cell
Endothelial cell
Kidney collecting duct intercalated cell
Mesangial cell
Kidney distal 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
Github:marshalljamie/Kidney-Slide-seq
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
Github:MacoskoLab/slideseq-tools
grekalab.org
GEO series:GSE190094
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
Basal cell of epithelium of bronchus
+7
Basal cell of epithelium of bronchus
Epithelial cell of lung
Epithelial cell of lung
62-year-old stage
+1
62-year-old stage
Normal
Normal
Male
Male
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Basal cell of epithelium of bronchus
Respiratory tract suprabasal cell
Epithelial cell of lung
Multiciliated epithelial cell
Lung secretory cell
Bronchial goblet cell
Squamous epithelial cell
Deuterosomal cell
Tissue
Epithelial cell of lung
Developmental stage
62-year-old stage
34-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
GEO series:GSE243045
EGA dataset:EGAD00001011362
CELLxGENE
10,099 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Oligodendrocyte
+25
Oligodendrocyte
Medial zone of hypothalamus
Medial zone of hypothalamus
42-year-old stage
42-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Oligodendrocyte
Astrocyte
T cell
Medial ganglionic eminence derived interneuron
Pvalb chandelier gabaergic interneuron
Microglial cell
Oligodendrocyte precursor cell
Neuron
Ependymal cell
Pericyte
Committed oligodendrocyte precursor
Monocyte
Cerebellar inhibitory gabaergic interneuron
Cerebral cortex neuron
Cerebellar granule cell
Intratelencephalic-projecting glutamatergic cortical neuron
Vascular associated smooth muscle cell
Endothelial cell
Caudal ganglionic eminence derived interneuron
Thalamic excitatory neuron
Central nervous system macrophage
Midbrain-derived inhibitory neuron
Fibroblast
Lamp5 lhx6 neuron
Mammillary body neuron
Near-projecting glutamatergic cortical neuron
Tissue
Medial zone of hypothalamus
Developmental stage
42-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
Single Cell Portal
10,086 cells
Explore
Mus musculus
Mus musculus
B cell
+8
B cell
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
B cell
Smooth muscle cell
Macrophage
Erythrocyte
Calvarial osteoblast
Endothelial cell
Granulocyte
Chondrocyte
Preosteoblast
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
CELLxGENE
10,019 cells
•
Yayon et al., 2024
A spatial human thymus cell atlas mapped to a continuous tissue axis
Explore
h5ad
Homo sapiens
Homo sapiens
Pericyte
+1
Pericyte
Thymus
Thymus
14th week post-fertilization stage
+11
14th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 5' v2
+3
10x 5' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Pericyte
Smooth muscle cell
Tissue
Thymus
Developmental stage
14th week post-fertilization stage
10-month-old stage
15th week post-fertilization stage
6-month-old stage
20th week post-fertilization stage
24th week post-fertilization stage
13th week post-fertilization stage
12th week post-fertilization stage
18th week post-fertilization stage
17th week post-fertilization stage
3-month-old stage
Newborn stage (0-28 days)
Disease
Normal
Sex
Female
Male
Technology
10x 5' v2
10x 3' v2
10x 5' v1
10x 3' v3
Suspension type
Cell
Related Links
Github:Teichlab/thymus_spatial_atlas/tree/main
ENA Project:PRJEB77091
EGA dataset:EGAD00001015384
ebi.ac.uk
GEO series:GSE271304
GEO series:GSE206710
ccgg.ugent.be
Github:Teichlab/TissueTag
Bioimage Archive:S-BIAD1257
CELLxGENE
10,016 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
Monocyte
+7
Monocyte
Liver
Liver
46-year-old stage
46-year-old stage
Breast cancer
Breast cancer
Female
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Monocyte
Malignant cell
Mature nk t cell
Macrophage
Blood vessel smooth muscle cell
Endothelial cell
Blood vessel endothelial cell
Fibroblast
Tissue
Liver
Developmental stage
46-year-old stage
Disease
Breast cancer
Sex
Female
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
humantumoratlas.org
dbGaP Study:phs002371
Single Cell Portal
10,006 cells
Explore
Macaca fascicularis
Macaca fascicularis
Pulmonary alveolar type 2 cell
+10
Pulmonary alveolar type 2 cell
Tuberculosis
Tuberculosis
Seq-well
Seq-well
Organism
Macaca fascicularis
Cell type
Pulmonary alveolar type 2 cell
T cell
Club cell
B cell
Neutrophil
Macrophage
Plasmacytoid dendritic cell, human
Endothelial cell
Fibroblast
Plasma cell
Mast cell
Tissue
Developmental stage
Disease
Tuberculosis
Sex
Technology
Seq-well
Suspension type
CELLxGENE
9,958 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
+8
T cell
Liver
Liver
44-year-old stage
44-year-old stage
Breast cancer
Breast cancer
Female
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
T cell
B cell
Malignant cell
Mature nk t cell
Macrophage
Blood vessel smooth muscle cell
Blood vessel endothelial cell
Fibroblast
Plasma cell
Tissue
Liver
Developmental stage
44-year-old stage
Disease
Breast cancer
Sex
Female
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
humantumoratlas.org
dbGaP Study:phs002371
CELLxGENE
9,957 cells
•
Arutyunyan et al., 2023
Spatial multiomics map of trophoblast development in early pregnancy
Explore
h5ad
Homo sapiens
Homo sapiens
Extravillous trophoblast
+1
Extravillous trophoblast
Trophoblast cell
Trophoblast cell
Normal
Normal
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Extravillous trophoblast
Placental villous trophoblast
Tissue
Trophoblast cell
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
Cell
Related Links
reproductivecellatlas.org
ArrayExpress BioStudies:E-MTAB-12595
EGA dataset:EGAD00001010037
EGA dataset:EGAD00001010038
Bioimage Archive:S-BIAD615
ArrayExpress BioStudies:E-MTAB-12650
ArrayExpress BioStudies:E-MTAB-12698
ArrayExpress BioStudies:E-MTAB-12421
EGA dataset:EGAD00001010017
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