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Tissue
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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
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Most cells
Fewest cells
2346
datasets
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
Neural cell
+6
Neural cell
Choroid plexus
Choroid plexus
66-year-old stage
+12
66-year-old stage
Covid-19
+3
Covid-19
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Neural cell
Ependymal cell
Macrophage
Glial cell
Mesenchymal cell
Choroid plexus epithelial cell
Cerebral cortex endothelial cell
Tissue
Choroid plexus
Developmental stage
66-year-old stage
69-year-old stage
91-year-old stage
71-year-old stage
85-year-old stage
68-year-old stage
55-year-old stage
84-year-old stage
57-year-old stage
74-year-old stage
60-year-old stage
78-year-old stage
79-year-old stage
Disease
Covid-19
Aspiration pneumonia
Influenza
Malignant pancreatic neoplasm
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
twc-stanford.shinyapps.io
ccb.uni-saarland.de
web.stanford.edu
HumanCellAtlas:72ff4818-5692-4bbc-8886-e47763531023
GEO series:GSE159812
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
Podocyte
+12
Podocyte
Kidney
Kidney
6-month-old stage
6-month-old stage
Normal
Normal
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 granular 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
Normal
Sex
Male
Technology
Slide-seqv2
Suspension type
Related Links
GEO series:GSE190094
Github:marshalljamie/Kidney-Slide-seq
Github:MacoskoLab/slideseq-tools
grekalab.org
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
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
Podocyte
+12
Podocyte
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
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
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
GEO series:GSE190094
Github:marshalljamie/Kidney-Slide-seq
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
Github:MacoskoLab/slideseq-tools
grekalab.org
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
Podocyte
+13
Podocyte
Cortex of kidney
Cortex of kidney
61-year-old stage
+4
61-year-old stage
Normal
Normal
Female
+1
Female
10x scatac-seq
10x scatac-seq
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Podocyte
Renal principal cell
Parietal epithelial cell
Renal beta-intercalated cell
Leukocyte
Kidney capillary endothelial cell
Epithelial cell of proximal tubule
Connective tissue cell
Renal alpha-intercalated cell
Kidney distal convoluted tubule epithelial cell
Kidney connecting tubule epithelial cell
Kidney loop of henle thick ascending limb epithelial cell
Kidney proximal straight tubule epithelial cell
Kidney proximal convoluted tubule epithelial cell
Tissue
Cortex of kidney
Developmental stage
61-year-old stage
52-year-old stage
54-year-old stage
50-year-old stage
62-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
HumanCellAtlas:2af52a13-65cb-4973-b513-39be38f2df3f
Github:p4rkerw/Muto_Wilson_NComm_2020
protocols.io:nuclei-isolation-from-human-kidney-for-single-nucl-nahdab6
GEO series:GSE151302
Kidney Online Transcriptomics
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 fat
+1
Visceral fat
34-year-old stage
+12
34-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 fat
Visceral abdominal adipose tissue
Developmental stage
34-year-old stage
53-year-old stage
68-year-old stage
48-year-old stage
29-year-old stage
28-year-old stage
24-year-old stage
35-year-old stage
Adult stage
33-year-old stage
41-year-old stage
36-year-old stage
73-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
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
Hemocyte
+2
Hemocyte
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
Hemocyte
Adult alary muscle cell
Sensory neuron
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
Cd8-positive, alpha-beta t cell
+5
Cd8-positive, alpha-beta t cell
Tonsil
Tonsil
Adult stage
Adult stage
Normal
Normal
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
Cd8-positive, alpha-beta t cell
Cd4-positive helper t cell
Regulatory t cell
Myeloid cell
B cell
Dendritic 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
Podocyte
+13
Podocyte
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
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
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
Placental villous trophoblast
Syncytiotrophoblast cell
Tissue
Trophoblast
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
Cell
Related Links
reproductivecellatlas.org
ArrayExpress BioStudies:E-MTAB-12421
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
EGA dataset:EGAD00001010017
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
Podocyte
+13
Podocyte
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
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
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
Github:MacoskoLab/slideseq-tools
grekalab.org
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
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
Stromal cell of endometrium
+15
Stromal cell of endometrium
Endometrium
+1
Endometrium
28-year-old stage
+2
28-year-old stage
Normal
Normal
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Stromal cell of endometrium
Stromal cell
Endothelial cell of venule
Perivascular cell
Uterine smooth muscle cell
Endothelial cell of artery
Leukocyte
Epithelial cell
Endothelial cell of uterus
Myoepithelial cell
Glandular secretory epithelial cell
Fibro/adipogenic progenitor cell
Ciliated epithelial cell
Circulating fibrocyte
Decidual cell
Fibroblast
Tissue
Endometrium
Myometrium
Developmental stage
28-year-old stage
32-year-old stage
31-year-old stage
Disease
Normal
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE260658
ArrayExpress BioStudies:E-MTAB-10287
GEO series:GSE111976
CELLxGENE
26,601 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 abdominal adipose tissue
+1
Subcutaneous abdominal adipose tissue
34-year-old stage
+12
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 abdominal adipose tissue
Subcutaneous adipose tissue
Developmental stage
34-year-old stage
53-year-old stage
68-year-old stage
29-year-old stage
51-year-old stage
57-year-old stage
24-year-old stage
35-year-old stage
58-year-old stage
33-year-old stage
41-year-old stage
36-year-old stage
73-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
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