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Technology
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Cell
890
Nucleus
655
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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
38,259 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Astrocyte
+9
Astrocyte
Inferior frontal gyrus
Inferior frontal gyrus
50-year-old stage
+2
50-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Astrocyte
Oligodendrocyte precursor cell
Oligodendrocyte
Leukocyte
Vascular associated smooth muscle cell
Fibroblast
Pericyte
Endothelial cell
Neuron
Central nervous system macrophage
Tissue
Inferior frontal gyrus
Developmental stage
50-year-old stage
42-year-old stage
29-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
NeMo archive:biccn/grant/u01_lein/linnarsson/transcriptome/sncell/10x_v3/human/raw
Github:linnarsson-lab/adult-human-brain
Github:linnarsson-lab/auto-annotation-ah
CELLxGENE
38,217 cells
•
Yang et al., 2021
Dysregulation of brain and choroid plexus cell types in severe COVID-19
Explore
h5ad
Homo sapiens
Homo sapiens
L2/3 intratelencephalic projecting glutamatergic neuron
+12
L2/3 intratelencephalic projecting glutamatergic neuron
Medial orbital frontal cortex
Medial orbital frontal cortex
82-year-old stage
+13
82-year-old stage
Tongue cancer
+8
Tongue cancer
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
L2/3 intratelencephalic projecting glutamatergic neuron
Cerebral cortex gabaergic interneuron
Cerebral cortex neuron
Astrocyte
Oligodendrocyte precursor cell
Oligodendrocyte
Sst gabaergic interneuron
L5/6 near-projecting glutamatergic neuron
Microglial cell
Endothelial cell
L4 intratelencephalic projecting glutamatergic neuron
Vip gabaergic interneuron
Pvalb gabaergic interneuron
Tissue
Medial orbital frontal cortex
Developmental stage
82-year-old stage
66-year-old stage
79-year-old stage
77-year-old stage
57-year-old stage
60-year-old stage
78-year-old stage
63-year-old stage
58-year-old stage
68-year-old stage
90-year-old stage
69-year-old stage
55-year-old stage
83-year-old stage
Disease
Tongue cancer
Small cell lung carcinoma
Breast cancer
Heart disorder
Influenza
Chronic obstructive pulmonary disease
Cardiomyopathy
Myocardial infarction
Covid-19
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
38,205 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Astrocyte
+10
Astrocyte
Substantia innominata
Substantia innominata
50-year-old stage
+2
50-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Astrocyte
Oligodendrocyte precursor cell
Oligodendrocyte
Leukocyte
Vascular associated smooth muscle cell
Fibroblast
Ependymal cell
Pericyte
Endothelial cell
Neuron
Central nervous system macrophage
Tissue
Substantia innominata
Developmental stage
50-year-old stage
42-year-old stage
29-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
NeMo archive:biccn/grant/u01_lein/linnarsson/transcriptome/sncell/10x_v3/human/raw
Github:linnarsson-lab/adult-human-brain
Github:linnarsson-lab/auto-annotation-ah
CELLxGENE
38,188 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Astrocyte
+9
Astrocyte
Primary somatosensory cortex
Primary somatosensory cortex
50-year-old stage
+2
50-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Astrocyte
Oligodendrocyte precursor cell
Oligodendrocyte
Leukocyte
Vascular associated smooth muscle cell
Fibroblast
Pericyte
Endothelial cell
Neuron
Central nervous system macrophage
Tissue
Primary somatosensory cortex
Developmental stage
50-year-old stage
42-year-old stage
29-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
NeMo archive:biccn/grant/u01_lein/linnarsson/transcriptome/sncell/10x_v3/human/raw
Github:linnarsson-lab/adult-human-brain
Github:linnarsson-lab/auto-annotation-ah
CELLxGENE
38,024 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
+14
Kidney loop of henle thick ascending limb epithelial cell
Cortex of kidney
Cortex of kidney
62-year-old stage
62-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 connecting tubule epithelial cell
Parietal epithelial cell
Leukocyte
Kidney distal convoluted tubule epithelial cell
Kidney interstitial fibroblast
Kidney collecting duct principal cell
Kidney loop of henle thin descending limb epithelial cell
Blood vessel smooth muscle cell
Kidney collecting duct intercalated cell
Podocyte
Pericyte
Endothelial cell
Mesangial cell
Kidney proximal convoluted tubule epithelial cell
Tissue
Cortex of kidney
Developmental stage
62-year-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
37,911 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Astrocyte
+10
Astrocyte
Hippocampal field
Hippocampal field
42-year-old stage
+1
42-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Astrocyte
Oligodendrocyte precursor cell
Oligodendrocyte
Leukocyte
Vascular associated smooth muscle cell
Fibroblast
Ependymal cell
Pericyte
Endothelial cell
Neuron
Central nervous system macrophage
Tissue
Hippocampal field
Developmental stage
42-year-old stage
29-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
NeMo archive:biccn/grant/u01_lein/linnarsson/transcriptome/sncell/10x_v3/human/raw
Github:linnarsson-lab/adult-human-brain
Github:linnarsson-lab/auto-annotation-ah
CELLxGENE
37,879 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
+9
Subcutaneous adipocyte
Subcutaneous adipose tissue
Subcutaneous adipose tissue
33-year-old stage
+3
33-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Subcutaneous adipocyte
Mural cell
Endothelial cell of lymphatic vessel
Macrophage
Mast cell
Endothelial cell
B cell
Dendritic cell
T cell
Mesenchymal stem cell of adipose tissue
Tissue
Subcutaneous adipose tissue
Developmental stage
33-year-old stage
34-year-old stage
24-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
37,809 cells
•
Pelka et al., 2021
Spatially organized multicellular immune hubs in human colorectal cancer
Explore
h5ad
Homo sapiens
Homo sapiens
Igg plasma cell
+1
Igg plasma cell
Colorectum
Colorectum
91-year-old stage
+33
91-year-old stage
Normal
+1
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Igg plasma cell
Iga plasma cell
Tissue
Colorectum
Developmental stage
91-year-old stage
82-year-old stage
70-year-old stage
77-year-old stage
50-year-old stage
57-year-old stage
76-year-old stage
62-year-old stage
52-year-old stage
60-year-old stage
48-year-old stage
64-year-old stage
89-year-old stage
45-year-old stage
67-year-old stage
71-year-old stage
78-year-old stage
36-year-old stage
59-year-old stage
47-year-old stage
56-year-old stage
58-year-old stage
61-year-old stage
51-year-old stage
49-year-old stage
42-year-old stage
35-year-old stage
53-year-old stage
72-year-old stage
73-year-old stage
90-year-old stage
69-year-old stage
81-year-old stage
55-year-old stage
Disease
Normal
Colon adenocarcinoma
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
BroadInstitute Single-Cell Portal:SCP1162/human-colon-cancer-atlas-c295#study-visualize
broad.io
GEO series:GSE178341
dbGaP Study:phs002407
HumanCellAtlas:6f03e4ad-9305-4bfa-a5b6-929ffb1d94bd
CELLxGENE
37,767 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Astrocyte
+9
Astrocyte
Brodmann (1909) area 25
Brodmann (1909) area 25
50-year-old stage
+2
50-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Astrocyte
Oligodendrocyte precursor cell
Oligodendrocyte
Leukocyte
Vascular associated smooth muscle cell
Fibroblast
Pericyte
Endothelial cell
Neuron
Central nervous system macrophage
Tissue
Brodmann (1909) area 25
Developmental stage
50-year-old stage
42-year-old stage
29-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
Github:linnarsson-lab/adult-human-brain
Github:linnarsson-lab/auto-annotation-ah
NeMo archive:biccn/grant/u01_lein/linnarsson/transcriptome/sncell/10x_v3/human/raw
CELLxGENE
37,747 cells
•
Wilson et al., 2022
Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression
Explore
h5ad
Homo sapiens
Homo sapiens
Kidney loop of henle thick ascending limb epithelial cell
+15
Kidney loop of henle thick ascending limb epithelial cell
Cortex of kidney
Cortex of kidney
57-year-old stage
+7
57-year-old stage
Normal
+1
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
Parietal epithelial cell
Kidney distal convoluted tubule epithelial cell
Renal beta-intercalated cell
Renal principal cell
Mononuclear leukocyte
Epithelial cell of proximal tubule
Fibroblast
Podocyte
Endothelial cell
B cell
Kidney proximal straight tubule epithelial cell
T cell
Kidney proximal convoluted tubule epithelial cell
Renal alpha-intercalated cell
Kidney loop of henle thin ascending limb epithelial cell
Tissue
Cortex of kidney
Developmental stage
57-year-old stage
52-year-old stage
74-year-old stage
78-year-old stage
59-year-old stage
61-year-old stage
51-year-old stage
53-year-old stage
Disease
Normal
Type 2 diabetes mellitus
Sex
Female
Male
Technology
10x scatac-seq
Suspension type
Nucleus
Related Links
GEO series:GSE195460
GEO series:GSE151302
GEO series:GSE131882
Kidney Online Transcriptomics
Github:p4rkerw/SALSA
HumanCellAtlas:3d49e5e5-976f-44cb-b6b9-079016c31c56
Github:p4rkerw/Wilson_Muto_NComm_2022
CELLxGENE
37,742 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
37,717 cells
•
Acera-Mateos et al., 2025
Systematic evaluation of single-cell multimodal data integration for comprehensive human reference atlas
Explore
h5ad
Homo sapiens
Homo sapiens
Kidney loop of henle thick ascending limb epithelial cell
+32
Kidney loop of henle thick ascending limb epithelial cell
Cortex of kidney
Cortex of kidney
50-year-old stage
+8
50-year-old stage
Normal
Normal
Female
+1
Female
10x multiome
10x multiome
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Kidney loop of henle thick ascending limb epithelial cell
Kidney outer medulla collecting duct intercalated cell
Endothelial cell of lymphatic vessel
Kidney connecting tubule epithelial cell
Parietal epithelial cell
Kidney connecting tubule principal cell
Non-classical monocyte
Endothelial cell of arteriole
Lymphocyte
Kidney collecting duct alpha-intercalated cell
Renal interstitial pericyte
Neutrophil
Kidney interstitial alternatively activated macrophage
Macula densa epithelial cell
Vasa recta ascending limb cell
Myeloid dendritic cell
Renal beta-intercalated cell
Renal principal cell
Epithelial cell of proximal tubule
Vascular associated smooth muscle cell
Fibroblast
Podocyte
Glomerular capillary endothelial cell
B cell
Epithelial cell of early distal convoluted tubule
Plasma cell
Peritubular capillary endothelial cell
Mesangial cell
T cell
Vasa recta descending limb cell
Plasmacytoid dendritic cell
Kidney proximal convoluted tubule epithelial cell
Epithelial cell of proximal tubule segment 3
Tissue
Cortex of kidney
Developmental stage
50-year-old stage
57-year-old stage
74-year-old stage
67-year-old stage
59-year-old stage
68-year-old stage
53-year-old stage
72-year-old stage
69-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x multiome
Suspension type
Nucleus
1
2
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