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Cell Type
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Disease
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Sex
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Technology
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Cell
934
Nucleus
679
Data Source
0
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ASAP
79
Bgee
40
CELLxGENE
2,213
Single Cell Portal
183
Sort
Most cells
Fewest cells
2515
datasets
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
GSE267511
Github
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
GSE295164
Processed Data
Saunders el al. (2023) Nature
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
phs002371
ASAP
v5
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
Fat cell
+12
Fat 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
Fat cell
Somatic precursor cell
Midgut large flat cell
Enteroendocrine cell
Adult midgut enterocyte
Copper cell
Epithelial cell
Muscle cell
Enterocyte of anterior adult midgut epithelium
Intestinal stem cell
Enterocyte of posterior adult midgut epithelium
Enteroblast
Adult differentiating enterocyte
Tissue
Gut
Developmental stage
Day 5 of adulthood
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Related Links
ebi.ac.uk
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
11,756 cells
•
Article
Explore
h5ad
Mus musculus
Mus musculus
T cell
+22
T cell
Ovary
Ovary
3-month-old stage
3-month-old stage
Normal
Normal
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
T cell
Granulosa cell
Blood vessel endothelial cell
Stromal cell
Endothelial cell of lymphatic vessel
Cumulus granulosa cell
Mast cell
Smooth muscle cell
Steroidogenic stromal cell of ovary
Endothelial cell of vascular tree
Ovarian surface epithelial cell
Adipocyte
Macrophage
Oviduct secretory cell
Plasma cell
Oocyte
Late luteal cell
Atretic granulosa cell
Early luteal cell
Theca cell
Dendritic cell
Ovarian fibroblast
Mural granulosa cell
Tissue
Ovary
Developmental stage
3-month-old stage
Disease
Normal
Sex
Female
Technology
Slide-seqv2
Suspension type
CELLxGENE
11,730 cells
•
Article
Explore
h5ad
Mus musculus
Mus musculus
T cell
+22
T cell
Ovary
Ovary
9-month-old stage
9-month-old stage
Normal
Normal
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
T cell
Granulosa cell
Blood vessel endothelial cell
Stromal cell
Endothelial cell of lymphatic vessel
Cumulus granulosa cell
Mast cell
Smooth muscle cell
Steroidogenic stromal cell of ovary
Endothelial cell of vascular tree
Ovarian surface epithelial cell
Adipocyte
Macrophage
Oviduct secretory cell
Plasma cell
Oocyte
Late luteal cell
Atretic granulosa cell
Early luteal cell
Theca cell
Dendritic cell
Ovarian fibroblast
Mural granulosa cell
Tissue
Ovary
Developmental stage
9-month-old stage
Disease
Normal
Sex
Female
Technology
Slide-seqv2
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
retina-atac.cells.ucsc.edu
explore.data.humancellatlas.org
GSE226108
CELLxGENE
11,608 cells
•
Article
Explore
h5ad
Mus musculus
Mus musculus
T cell
+22
T cell
Ovary
Ovary
12-month-old stage
12-month-old stage
Normal
Normal
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
T cell
Granulosa cell
Blood vessel endothelial cell
Stromal cell
Endothelial cell of lymphatic vessel
Cumulus granulosa cell
Mast cell
Smooth muscle cell
Steroidogenic stromal cell of ovary
Endothelial cell of vascular tree
Ovarian surface epithelial cell
Adipocyte
Macrophage
Oviduct secretory cell
Plasma cell
Oocyte
Late luteal cell
Atretic granulosa cell
Early luteal cell
Theca cell
Dendritic cell
Ovarian fibroblast
Mural granulosa cell
Tissue
Ovary
Developmental stage
12-month-old stage
Disease
Normal
Sex
Female
Technology
Slide-seqv2
Suspension type
CELLxGENE
11,574 cells
•
Szabo et al., 2021
Longitudinal profiling of respiratory and systemic immune responses reveals myeloid cell-driven lung inflammation in severe COVID-19
Explore
h5ad
Homo sapiens
Homo sapiens
Neutrophil
+7
Neutrophil
Blood
Blood
49-year-old stage
49-year-old stage
Covid-19
Covid-19
Male
Male
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Neutrophil
Erythrocyte
Mature nk t cell
Platelet
Myeloid cell
Plasma cell
B cell
Dendritic cell
Tissue
Blood
Developmental stage
49-year-old stage
Disease
Covid-19
Sex
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
data.mendeley.com
github.com
covid19cellatlas.org
CELLxGENE
11,510 cells
•
Liu et al., 2022
Spatial maps of T cell receptors and transcriptomes reveal distinct immune niches and interactions in the adaptive immune response
Explore
h5ad
Mus musculus
Mus musculus
Natural killer cell
+5
Natural killer cell
Spleen
Spleen
Normal
Normal
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Natural killer cell
Cd8-positive, alpha-beta t cell
Cd4-positive helper t cell
Myeloid cell
B cell
Memory t cell
Tissue
Spleen
Developmental stage
Disease
Normal
Sex
Technology
Slide-seqv2
Suspension type
Related Links
singlecell.broadinstitute.org
github.com
CELLxGENE
11,484 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
40-year-old stage
40-year-old stage
Breast cancer
Breast cancer
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
T cell
Hepatocyte
Endothelial cell
Mature nk t cell
Macrophage
Plasma cell
Malignant cell
Monocyte
Fibroblast
Tissue
Liver
Developmental stage
40-year-old stage
Disease
Breast cancer
Sex
Female
Technology
Slide-seqv2
Suspension type
Related Links
humantumoratlas.org
phs002371
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