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Disease
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Technology
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Cell
896
Nucleus
659
Data Source
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Asap
43
Bgee
40
Cellxgene
2,080
Single cell portal
183
Sort
Most cells
Fewest cells
2346
datasets
CELLxGENE
12,330 cells
•
Escoubas et al., 2024
Type-I-interferon-responsive microglia shape cortical development and behavior
Explore
h5ad
Mus musculus
Mus musculus
Microglial cell
Microglial cell
Barrel cortex
Barrel cortex
5-day-old stage
+1
5-day-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Microglial cell
Tissue
Barrel cortex
Developmental stage
5-day-old stage
7-day-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
annamolofskylab.org
GEO series:GSE173173
lcdorman.shinyapps.io
CELLxGENE
12,295 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
T cell
+6
T cell
Mammary gland
Mammary gland
3-month-old stage
+2
3-month-old stage
Normal
Normal
Female
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Mus musculus
Cell type
T cell
Stromal cell
Endothelial cell
Basal cell
Luminal epithelial cell of mammary gland
Macrophage
B cell
Tissue
Mammary gland
Developmental stage
3-month-old stage
20-month-old stage and over
18-month-old stage
Disease
Normal
Sex
Female
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
protocols.io:smartseq2-for-htp-generation-of-facs-sorted-single-2uwgexe
Github:czbiohub/tabula-muris-senis
CELLxGENE
12,258 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
Endothelial cell of hepatic sinusoid
+10
Endothelial cell of hepatic sinusoid
Liver
Liver
31-year-old stage
31-year-old stage
Breast cancer
Breast cancer
Female
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Endothelial cell of hepatic sinusoid
T cell
Blood vessel endothelial cell
Hepatocyte
Mature nk t cell
Blood vessel smooth muscle cell
Hepatic stellate cell
Macrophage
Malignant cell
Neuron
Fibroblast
Tissue
Liver
Developmental stage
31-year-old stage
Disease
Breast cancer
Sex
Female
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
humantumoratlas.org
dbGaP Study:phs002371
CELLxGENE
12,205 cells
•
Lazarescu et al., 2025
Human subcutaneous and visceral adipocyte atlases uncover classical and nonclassical adipocytes and depot-specific patterns
Explore
h5ad
Homo sapiens
Homo sapiens
Subcutaneous adipocyte
Subcutaneous adipocyte
Subcutaneous adipose tissue
Subcutaneous adipose tissue
34-year-old stage
+3
34-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Subcutaneous adipocyte
Tissue
Subcutaneous adipose tissue
Developmental stage
34-year-old stage
24-year-old stage
33-year-old stage
41-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
DOI:10.5281/zenodo.14001210
GEO series:GSE281356
HumanCellAtlas:df8eb7ce-3707-46af-b823-e081a562e954
CELLxGENE
12,162 cells
•
Fink et al., 2022
Single-cell and spatial mapping Identify cell types and signaling Networks in the human ureter
Explore
h5ad
Homo sapiens
Homo sapiens
Central memory cd4-positive, alpha-beta t cell
+12
Central memory cd4-positive, alpha-beta t cell
Ureter
Ureter
69-year-old stage
+8
69-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Central memory cd4-positive, alpha-beta t cell
Effector cd8-positive, alpha-beta t cell
Mature nk t cell
Mast cell
Classical monocyte
Cd8-positive, alpha-beta memory t cell
Macrophage
Regulatory t cell
B cell
Mucosal invariant t cell
Double negative thymocyte
Dendritic cell
Non-classical monocyte
Tissue
Ureter
Developmental stage
69-year-old stage
75-year-old stage
65-year-old stage
85-year-old stage
68-year-old stage
82-year-old stage
81-year-old stage
74-year-old stage
79-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE184111
GEO series:GSE184112
UCSC Cell Browser:adult-ureter
Zenodo record:6762182
Github:2019surbhi/tinglab_ureter_analysis
CELLxGENE
12,132 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
6-month-old stage
6-month-old stage
Autosomal dominant polycystic kidney disease
Autosomal dominant polycystic 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
6-month-old stage
Disease
Autosomal dominant polycystic 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
12,118 cells
•
Easter et al., 2024
Single-cell and spatially resolved interactomics of tooth-associated keratinocytes in periodontitis
Explore
h5ad
Mus musculus
Mus musculus
Muscle cell
+7
Muscle cell
Gingiva
Gingiva
4-week-old stage
4-week-old stage
Normal
Normal
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Muscle cell
Gingival epithelial cell
Inflammatory cell
Endothelial cell of vascular tree
Mural cell
Glial cell
Fibroblast
Salivary gland cell
Tissue
Gingiva
Developmental stage
4-week-old stage
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE267511
Github:sequeira-science/Quinn_et_al_2024_NatComms_mousegingiva/tree/main
CELLxGENE
11,964 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
Sensory hair cell
+2
Sensory hair cell
Crista ampullaris
+4
Crista ampullaris
Pharyngula:prim-15
+9
Pharyngula:prim-15
Normal
Normal
Sci-rna-seq3
Sci-rna-seq3
Nucleus
Nucleus
Organism
Danio rerio
Cell type
Sensory hair cell
Neurecto-epithelial cell
Auditory epithelial supporting cell
Tissue
Crista ampullaris
Ear vesicle
Macula
Lateral line
Semicircular canal
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
11,851 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
+6
T cell
Liver
Liver
29-year-old stage
29-year-old stage
Breast cancer
Breast cancer
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
T cell
Hepatocyte
Endothelial cell
Macrophage
Malignant cell
Monocyte
Fibroblast
Tissue
Liver
Developmental stage
29-year-old stage
Disease
Breast cancer
Sex
Female
Technology
Slide-seqv2
Suspension type
Related Links
humantumoratlas.org
dbGaP Study:phs002371
ASAP
11,788 cells
•
Li et al., 2022
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly
Explore
h5ad
Drosophila melanogaster
Drosophila melanogaster
Enteroendocrine cell
+1
Enteroendocrine cell
Gut
Gut
Day 5 of adulthood
Day 5 of adulthood
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Organism
Drosophila melanogaster
Cell type
Enteroendocrine cell
Muscle cell
Tissue
Gut
Developmental stage
Day 5 of adulthood
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Related Links
ArrayExpress BioStudies:E-MTAB-10519
Single Cell Portal
11,765 cells
Explore
Mus musculus
Mus musculus
T cell
+5
T cell
Encephalitis
Encephalitis
10x 3' v3
10x 3' v3
Organism
Mus musculus
Cell type
T cell
Neutrophil
Natural killer cell
Macrophage
B cell
Monocyte
Tissue
Developmental stage
Disease
Encephalitis
Sex
Technology
10x 3' v3
Suspension type
CELLxGENE
11,617 cells
•
Liang et al., 2023
A multi-omics atlas of the human retina at single-cell resolution
Explore
h5ad
Homo sapiens
Homo sapiens
Retinal ganglion cell
Retinal ganglion cell
Peripheral region of retina
+2
Peripheral region of retina
65-year-old stage
+4
65-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Retinal ganglion cell
Tissue
Peripheral region of retina
Macula lutea proper
Fovea centralis
Developmental stage
65-year-old stage
84-year-old stage
78-year-old stage
73-year-old stage
83-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
UCSC Cell Browser:retina-atac
GEO series:GSE226108
HumanCellAtlas:9c20a245-f2c0-43ae-82c9-2232ec6b594f
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