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Cell Type
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Tissue
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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
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ASAP
79
Bgee
40
CELLxGENE
2,213
Single Cell Portal
183
Sort
Most cells
Fewest cells
2515
datasets
CELLxGENE
10,701 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
+13
Podocyte
Cortex of kidney
Cortex of kidney
64-year-old stage
64-year-old stage
Normal
Normal
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
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 granular cell
Kidney collecting duct principal cell
Kidney loop of henle thick ascending limb epithelial cell
Macula densa epithelial cell
Mesangial cell
Kidney proximal convoluted tubule epithelial cell
Tissue
Cortex of kidney
Developmental stage
64-year-old stage
Disease
Normal
Sex
Female
Technology
Slide-seqv2
Suspension type
Related Links
ncbi.nlm.nih.gov
Kidney Slide-seq Github
protocols.io
Macosko Lab Slide-seq Github
grekalab.org
CELLxGENE
10,696 cells
•
Chen et al., 2021
Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+6
T cell
Ascending colon
+6
Ascending colon
66-year-old stage
+26
66-year-old stage
Tubulovillous adenoma
+5
Tubulovillous adenoma
Female
+1
Female
Trudrop
Trudrop
Cell
Cell
Organism
Homo sapiens
Cell type
T cell
Endothelial cell
Mast cell
Myeloid cell
Plasma cell
B cell
Fibroblast
Tissue
Ascending colon
Hepatic flexure of colon
Rectum
Transverse colon
Descending colon
Sigmoid colon
Hepatic cecum
Developmental stage
66-year-old stage
69-year-old stage
65-year-old stage
71-year-old stage
53-year-old stage
52-year-old stage
54-year-old stage
68-year-old stage
56-year-old stage
55-year-old stage
50-year-old stage
51-year-old stage
57-year-old stage
72-year-old stage
74-year-old stage
58-year-old stage
59-year-old stage
67-year-old stage
64-year-old stage
62-year-old stage
70-year-old stage
46-year-old stage
60-year-old stage
63-year-old stage
76-year-old stage
73-year-old stage
40-year-old stage
Disease
Tubulovillous adenoma
Tubular adenoma
Colorectal cancer
Normal
Hyperplastic polyp
Colon sessile serrated adenoma/polyp
Sex
Female
Male
Technology
Trudrop
Suspension type
Cell
Related Links
explore.data.humancellatlas.org
phs002371
humantumoratlas.org
CELLxGENE
10,689 cells
•
Dong et al., 2024
Transcriptome Analysis of Archived Tumor Tissues by Visium, GeoMx DSP, and Chromium Methods Reveals Inter- and Intra-Patient Heterogeneity
Explore
h5ad
Homo sapiens
Homo sapiens
Granulocyte
+18
Granulocyte
Parenchyma of mammary gland
Parenchyma of mammary gland
Adult stage
Adult stage
Invasive ductal breast carcinoma
+1
Invasive ductal breast carcinoma
Female
Female
Cell
Cell
Organism
Homo sapiens
Cell type
Granulocyte
Dendritic cell, human
Natural killer cell
Cytotoxic t cell
Mast cell
Natural t-regulatory cell
Capillary endothelial cell
Classical monocyte
Smooth muscle cell
Plasmacytoid dendritic cell
Macrophage
Activated cd8-positive, alpha-beta t cell
Fibroblast of breast
Fibroblast of lung
Plasma cell
Malignant cell
Cd4-positive, alpha-beta memory t cell
Pericyte
Conventional dendritic cell
Tissue
Parenchyma of mammary gland
Developmental stage
Adult stage
Disease
Invasive ductal breast carcinoma
Invasive lobular breast carcinoma
Sex
Female
Technology
Suspension type
Cell
Related Links
E-MTAB-14560
E-MTAB-14566
github.com
ASAP
v5
10,686 cells
•
Li et al., 2022
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly
Explore
h5ad
Drosophila melanogaster
Drosophila melanogaster
Neuron
+13
Neuron
Heart
Heart
Day 5 of adulthood
Day 5 of adulthood
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Organism
Drosophila melanogaster
Cell type
Neuron
Adult abdominal pericardial cell
Indirect flight muscle cell
Fat cell
Cardial cell
Tracheolar cell
Hemocyte
Epithelial cell
Muscle cell
Adult tracheocyte
Embryonic/larval crystal cell
Oenocyte
Adult oenocyte
Adult heart ventral longitudinal muscle cell
Tissue
Heart
Developmental stage
Day 5 of adulthood
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Related Links
ebi.ac.uk
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
data.nemoarchive.org
github (analysis and figures)
github (auto-annotations)
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
phs002371
CELLxGENE
10,570 cells
•
Article
Explore
h5ad
Mus musculus
Mus musculus
Granulosa cell
+21
Granulosa cell
Ovary
Ovary
3-month-old stage
3-month-old stage
Normal
Normal
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
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
10,567 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
10,553 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
10,549 cells
•
Article
Explore
h5ad
Mus musculus
Mus musculus
T cell
+21
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
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
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
GSE295164
Processed Data
Saunders el al. (2023) Nature
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.com
Human Cell Atlas
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