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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
890
Nucleus
655
Data Source
0
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Asap
43
Bgee
40
Cellxgene
2,066
Single cell portal
179
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Most cells
Fewest cells
2328
datasets
CELLxGENE
27,108 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Smooth muscle cell of the pulmonary artery
+28
Smooth muscle cell of the pulmonary artery
Sinoatrial node
Sinoatrial node
Fifth decade stage
+1
Fifth decade stage
Normal
Normal
Female
+1
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Smooth muscle cell of the pulmonary artery
Capillary endothelial cell
Endothelial cell of lymphatic vessel
Glial cell
Macrophage
Naive thymus-derived cd4-positive, alpha-beta t cell
Endocardial cell
Mucosal invariant t cell
Mast cell
Cd16-negative, cd56-bright natural killer cell, human
Adipocyte
Neutrophil
Monocyte
Cd14-positive monocyte
Cd8-positive, alpha-beta cytotoxic t cell
Vein endothelial cell
Dendritic cell, human
Regular atrial cardiac myocyte
Pericyte
Endothelial cell
Cardiac pacemaker cell of sinoatrial node
B cell
Cd8-positive, alpha-beta t cell
Activated cd4-positive, alpha-beta t cell
Plasma cell
Fibroblast of cardiac tissue
Cd14-low, cd16-positive monocyte
Smooth muscle cell
Endothelial cell of artery
Tissue
Sinoatrial node
Developmental stage
Fifth decade stage
Third decade stage
Disease
Normal
Sex
Female
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
heartcellatlas.org
ArrayExpress BioStudies:E-MTAB-12916
ArrayExpress BioStudies:E-MTAB-12975
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
ArrayExpress BioStudies:E-MTAB-12919
CELLxGENE
27,092 cells
•
Yang et al., 2021
Dysregulation of brain and choroid plexus cell types in severe COVID-19
Explore
h5ad
Homo sapiens
Homo sapiens
Cerebral cortex endothelial cell
+6
Cerebral cortex endothelial cell
Choroid plexus
Choroid plexus
85-year-old stage
+12
85-year-old stage
Malignant pancreatic neoplasm
+3
Malignant pancreatic neoplasm
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Cerebral cortex endothelial cell
Glial cell
Macrophage
Ependymal cell
Mesenchymal cell
Choroid plexus epithelial cell
Neural cell
Tissue
Choroid plexus
Developmental stage
85-year-old stage
91-year-old stage
66-year-old stage
79-year-old stage
57-year-old stage
60-year-old stage
74-year-old stage
71-year-old stage
78-year-old stage
68-year-old stage
84-year-old stage
69-year-old stage
55-year-old stage
Disease
Malignant pancreatic neoplasm
Aspiration pneumonia
Influenza
Covid-19
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
GEO series:GSE159812
twc-stanford.shinyapps.io
ccb.uni-saarland.de
web.stanford.edu
HumanCellAtlas:72ff4818-5692-4bbc-8886-e47763531023
CELLxGENE
27,044 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
+12
Kidney loop of henle thick ascending limb epithelial cell
Kidney
Kidney
6-month-old stage
6-month-old stage
Normal
Normal
Male
Male
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Kidney loop of henle thick ascending limb epithelial cell
Kidney granular cell
Leukocyte
Macrophage
Kidney distal convoluted tubule epithelial cell
Kidney interstitial fibroblast
Kidney collecting duct principal cell
Blood vessel smooth muscle cell
Kidney collecting duct intercalated cell
Podocyte
Endothelial cell
Mesangial cell
Kidney proximal convoluted tubule epithelial cell
Tissue
Kidney
Developmental stage
6-month-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
27,036 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
Kidney loop of henle thick ascending limb epithelial cell
+12
Kidney loop of henle thick ascending limb epithelial cell
Cortex of kidney
Cortex of kidney
72-year-old stage
72-year-old stage
Normal
Normal
Male
Male
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
Kidney loop of henle thick ascending limb epithelial cell
Kidney granular cell
Leukocyte
Macrophage
Kidney distal convoluted tubule epithelial cell
Kidney interstitial fibroblast
Kidney collecting duct principal cell
Blood vessel smooth muscle cell
Kidney collecting duct intercalated cell
Podocyte
Endothelial cell
Mesangial cell
Kidney proximal convoluted tubule epithelial cell
Tissue
Cortex of kidney
Developmental stage
72-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
27,034 cells
•
Muto et al., 2021
Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney
Explore
h5ad
Homo sapiens
Homo sapiens
Kidney loop of henle thick ascending limb epithelial cell
+13
Kidney loop of henle thick ascending limb epithelial cell
Cortex of kidney
Cortex of kidney
50-year-old stage
+4
50-year-old stage
Normal
Normal
Female
+1
Female
10x scatac-seq
10x scatac-seq
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Kidney loop of henle thick ascending limb epithelial cell
Kidney connecting tubule epithelial cell
Parietal epithelial cell
Leukocyte
Kidney distal convoluted tubule epithelial cell
Renal beta-intercalated cell
Renal principal cell
Epithelial cell of proximal tubule
Podocyte
Kidney capillary endothelial cell
Kidney proximal straight tubule epithelial cell
Connective tissue cell
Kidney proximal convoluted tubule epithelial cell
Renal alpha-intercalated cell
Tissue
Cortex of kidney
Developmental stage
50-year-old stage
62-year-old stage
52-year-old stage
54-year-old stage
61-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x scatac-seq
Suspension type
Nucleus
Related Links
genome.ucsc.edu
UCSC Cell Browser:human-kidney-atac
Github:p4rkerw/Muto_Wilson_NComm_2020
Kidney Online Transcriptomics
GEO series:GSE151302
HumanCellAtlas:2af52a13-65cb-4973-b513-39be38f2df3f
protocols.io:nuclei-isolation-from-human-kidney-for-single-nucl-nahdab6
CELLxGENE
26,935 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
Adipocyte of omentum tissue
Adipocyte of omentum tissue
Visceral abdominal adipose tissue
+1
Visceral abdominal adipose tissue
48-year-old stage
+12
48-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Adipocyte of omentum tissue
Tissue
Visceral abdominal adipose tissue
Visceral fat
Developmental stage
48-year-old stage
33-year-old stage
Adult stage
28-year-old stage
36-year-old stage
68-year-old stage
34-year-old stage
35-year-old stage
53-year-old stage
73-year-old stage
24-year-old stage
29-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
HumanCellAtlas:df8eb7ce-3707-46af-b823-e081a562e954
GEO series:GSE281356
ASAP
26,926 cells
•
Li et al., 2022
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly
Explore
h5ad
Drosophila melanogaster
Drosophila melanogaster
Adult alary muscle cell
+2
Adult alary muscle cell
Fat body
Fat body
Day 3 of adulthood
Day 3 of adulthood
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Organism
Drosophila melanogaster
Cell type
Adult alary muscle cell
Sensory neuron
Hemocyte
Tissue
Fat body
Developmental stage
Day 3 of adulthood
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Related Links
ArrayExpress BioStudies:E-MTAB-10519
CELLxGENE
26,917 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
Homo sapiens
Homo sapiens
Cd4-positive helper t cell
+5
Cd4-positive helper t cell
Tonsil
Tonsil
Adult stage
Adult stage
Normal
Normal
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
Cd4-positive helper t cell
B cell
Cd8-positive, alpha-beta t cell
Dendritic cell
Regulatory t cell
Myeloid cell
Tissue
Tonsil
Developmental stage
Adult stage
Disease
Normal
Sex
Technology
Slide-seqv2
Suspension type
Related Links
Github:soph-liu/Slide-TCR-seq
BroadInstitute Single-Cell Portal:SCP1348/slide-tcr-seq-data
CELLxGENE
26,889 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
+13
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 granular cell
Leukocyte
Macrophage
Kidney distal convoluted tubule epithelial cell
Kidney interstitial fibroblast
Kidney collecting duct principal cell
Macula densa epithelial cell
Blood vessel smooth muscle cell
Kidney collecting duct intercalated cell
Podocyte
Endothelial 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
Github:marshalljamie/Kidney-Slide-seq
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
Github:MacoskoLab/slideseq-tools
grekalab.org
GEO series:GSE190094
CELLxGENE
26,853 cells
•
Arutyunyan et al., 2023
Spatial multiomics map of trophoblast development in early pregnancy
Explore
h5ad
Homo sapiens
Homo sapiens
Extravillous trophoblast
+2
Extravillous trophoblast
Trophoblast
Trophoblast
Normal
Normal
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Extravillous trophoblast
Syncytiotrophoblast cell
Placental villous trophoblast
Tissue
Trophoblast
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
Cell
Related Links
reproductivecellatlas.org
EGA dataset:EGAD00001010037
EGA dataset:EGAD00001010038
EGA dataset:EGAD00001010017
Bioimage Archive:S-BIAD615
ArrayExpress BioStudies:E-MTAB-12650
ArrayExpress BioStudies:E-MTAB-12421
ArrayExpress BioStudies:E-MTAB-12595
ArrayExpress BioStudies:E-MTAB-12698
CELLxGENE
26,750 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
+13
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 granular cell
Leukocyte
Macrophage
Kidney distal convoluted tubule epithelial cell
Kidney interstitial fibroblast
Kidney collecting duct principal cell
Macula densa epithelial cell
Blood vessel smooth muscle cell
Kidney collecting duct intercalated cell
Podocyte
Endothelial 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
26,694 cells
•
Ulrich et al., 2024
Cellular heterogeneity and dynamics of the human uterus in healthy premenopausal women
Explore
h5ad
Homo sapiens
Homo sapiens
Myoepithelial cell
+15
Myoepithelial cell
Endometrium
+1
Endometrium
32-year-old stage
+2
32-year-old stage
Normal
Normal
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Myoepithelial cell
Circulating fibrocyte
Ciliated epithelial cell
Leukocyte
Endothelial cell of uterus
Stromal cell of endometrium
Stromal cell
Glandular secretory epithelial cell
Epithelial cell
Endothelial cell of venule
Perivascular cell
Fibro/adipogenic progenitor cell
Fibroblast
Decidual cell
Endothelial cell of artery
Uterine smooth muscle cell
Tissue
Endometrium
Myometrium
Developmental stage
32-year-old stage
28-year-old stage
31-year-old stage
Disease
Normal
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE260658
GEO series:GSE111976
ArrayExpress BioStudies:E-MTAB-10287
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