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Tissue
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Developmental Stage
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Disease
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Technology
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Cell
893
Nucleus
659
Data Source
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Asap
43
Bgee
40
Cellxgene
2,077
Single cell portal
179
Sort
Most cells
Fewest cells
2339
datasets
CELLxGENE
13,161 cells
•
Fink et al., 2022
Single-cell and spatial mapping Identify cell types and signaling Networks in the human ureter
Explore
h5ad
Homo sapiens
Homo sapiens
Leukocyte
+7
Leukocyte
Ureter
Ureter
69-year-old stage
69-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Leukocyte
Intermediate cell of urothelium
Umbrella cell of urothelium
Monocyte
Smooth muscle cell
Basal cell of urothelium
Endothelial cell
Fibroblast
Tissue
Ureter
Developmental stage
69-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE184111
GEO series:GSE184112
UCSC Cell Browser:adult-ureter
Zenodo record:6762182
Github:2019surbhi/tinglab_ureter_analysis
CELLxGENE
13,147 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
+15
Kidney loop of henle thick ascending limb epithelial cell
Cortex of kidney
Cortex of kidney
75-year-old stage
75-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 interstitial fibroblast
Leukocyte
Kidney proximal convoluted tubule epithelial cell
Podocyte
Parietal epithelial cell
Pericyte
Kidney collecting duct principal cell
Blood vessel smooth muscle cell
Kidney loop of henle thin descending limb epithelial cell
Endothelial cell
Kidney loop of henle epithelial cell
Kidney collecting duct intercalated cell
Mesangial cell
Kidney connecting tubule epithelial cell
Kidney distal convoluted tubule epithelial cell
Tissue
Cortex of kidney
Developmental stage
75-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
ASAP
13,143 cells
•
Li et al., 2022
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly
Explore
h5ad
Drosophila melanogaster
Drosophila melanogaster
Muscle cell
+1
Muscle cell
Male reproductive gland
Male reproductive gland
Day 2 of adulthood
Day 2 of adulthood
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Organism
Drosophila melanogaster
Cell type
Muscle cell
Hemocyte
Tissue
Male reproductive gland
Developmental stage
Day 2 of adulthood
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Related Links
ArrayExpress BioStudies:E-MTAB-10519
CELLxGENE
12,964 cells
•
Santo et al., 2025
Exploring the utility of snRNA-seq in profiling human bladder tissue: A comprehensive comparison with scRNA-seq
Explore
h5ad
Homo sapiens
Homo sapiens
Schwann cell
+7
Schwann cell
Urinary bladder
Urinary bladder
21-year-old stage
21-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Cell
+1
Cell
Organism
Homo sapiens
Cell type
Schwann cell
Endothelial cell of artery
Endothelial cell of lymphatic vessel
Smooth muscle cell
Vascular associated smooth muscle cell
Endothelial cell
Vein endothelial cell
Fibroblast
Tissue
Urinary bladder
Developmental stage
21-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Cell
Nucleus
Related Links
Github:basanto/Human_Bladder_scRNA-seq_vs_snRNA-seq
GEO series:GSE267964
CELLxGENE
12,944 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Oligodendrocyte
+20
Oligodendrocyte
Centromedian nucleus of thalamus
Centromedian nucleus of thalamus
50-year-old stage
50-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Oligodendrocyte
Natural killer cell
Astrocyte
T cell
Medial ganglionic eminence derived interneuron
Pvalb chandelier gabaergic interneuron
Microglial cell
Oligodendrocyte precursor cell
B cell
Neuron
Pericyte
Committed oligodendrocyte precursor
Monocyte
Vascular associated smooth muscle cell
Endothelial cell
Caudal ganglionic eminence derived interneuron
Thalamic excitatory neuron
Central nervous system macrophage
Midbrain-derived inhibitory neuron
Fibroblast
Lamp5 lhx6 neuron
Tissue
Centromedian nucleus of thalamus
Developmental stage
50-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
Single Cell Portal
12,929 cells
Explore
Mus musculus
Mus musculus
Retinal ganglion cell
+9
Retinal ganglion cell
Normal
Normal
10x 3' v3
10x 3' v3
Organism
Mus musculus
Cell type
Retinal ganglion cell
Retinal blood vessel endothelial cell
Retinal cone cell
Mueller cell
Amacrine cell
Retina horizontal cell
Rod bipolar cell
Fibroblast
Retinal rod cell
Myeloid cell
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
Single Cell Portal
12,929 cells
Explore
Mus musculus
Mus musculus
Retinal ganglion cell
+9
Retinal ganglion cell
Normal
Normal
10x 3' v3
10x 3' v3
Organism
Mus musculus
Cell type
Retinal ganglion cell
Retinal blood vessel endothelial cell
Retinal cone cell
Mueller cell
Amacrine cell
Retina horizontal cell
Rod bipolar cell
Fibroblast
Retinal rod cell
Myeloid cell
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
CELLxGENE
12,918 cells
•
Yayon et al., 2024
A spatial human thymus cell atlas mapped to a continuous tissue axis
Explore
h5ad
Homo sapiens
Homo sapiens
Dendritic cell
+10
Dendritic cell
Thymus
Thymus
16th week post-fertilization stage
+4
16th week post-fertilization stage
Normal
Normal
Female
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Dendritic cell
T cell
B cell
Pericyte
Granulocyte monocyte progenitor cell
Smooth muscle cell
Macrophage
Erythrocyte
Endothelial cell
Epithelial cell
Fibroblast
Tissue
Thymus
Developmental stage
16th week post-fertilization stage
19th week post-fertilization stage
13th week post-fertilization stage
18th week post-fertilization stage
17th week post-fertilization stage
Disease
Normal
Sex
Female
Technology
Visium spatial gene expression v1
Suspension type
Related Links
Github:Teichlab/thymus_spatial_atlas/tree/main
Bioimage Archive:S-BIAD1257
ENA Project:PRJEB77091
ebi.ac.uk
GEO series:GSE271304
GEO series:GSE206710
ccgg.ugent.be
Github:Teichlab/TissueTag
EGA dataset:EGAD00001015384
CELLxGENE
12,906 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
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 interstitial fibroblast
Leukocyte
Kidney proximal convoluted tubule epithelial cell
Podocyte
Kidney collecting duct principal cell
Macrophage
Blood vessel smooth muscle cell
Endothelial cell
Kidney collecting duct intercalated cell
Mesangial cell
Kidney granular cell
Kidney distal 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
Single Cell Portal
12,868 cells
Explore
Mus musculus
Mus musculus
Obsolete excitatory neuron
+4
Obsolete excitatory neuron
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Obsolete excitatory neuron
Oligodendrocyte precursor cell
Brain microvascular endothelial cell
Obsolete inhibitory neuron
Astrocyte of the cerebellum
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
Related Links
Corresponding registered brain section (MD716) (section 214)
Corresponding registered brain section (MD716) (section 215)
Corresponding registered brain section (MD716) (section 216)
Corresponding registered brain section (MD716) (section 217)
Corresponding registered brain section (MD716) (section 218)
Corresponding registered brain section (MD716) (section 219)
CELLxGENE
12,822 cells
•
de Vrij et al., 2024
Persistent T cell unresponsiveness associated with chronic visceral leishmaniasis in HIV-coinfected patients
Explore
h5ad
Homo sapiens
Homo sapiens
Activated cd8-positive, alpha-beta t cell
+27
Activated cd8-positive, alpha-beta t cell
Blood
Blood
Fifth decade stage
+1
Fifth decade stage
Visceral leishmaniasis
+1
Visceral leishmaniasis
Male
Male
10x 5' v1
10x 5' v1
Cell
Cell
Organism
Homo sapiens
Cell type
Activated cd8-positive, alpha-beta t cell
Plasmacytoid dendritic cell
Natural killer cell
Naive thymus-derived cd4-positive, alpha-beta t cell
Erythroid lineage cell
Innate lymphoid cell
Effector memory cd8-positive, alpha-beta t cell
Regulatory t cell
Cd4-positive, alpha-beta memory t cell
Naive b cell
Memory b cell
Gamma-delta t cell
Cd4-positive, alpha-beta cytotoxic t cell
Monocyte
Platelet
Naive thymus-derived cd8-positive, alpha-beta t cell
Mature b cell
Cd16-negative, cd56-bright natural killer cell, human
Cd14-positive monocyte
Hematopoietic precursor cell
Activated cd4-positive, alpha-beta t cell
Cd4-negative, cd8-negative, alpha-beta intraepithelial t cell
Plasmablast
Effector memory cd4-positive, alpha-beta t cell
Cd8-positive, alpha-beta memory t cell
Mucosal invariant t cell
Cd16-positive, cd56-dim natural killer cell, human
Cd1c-positive myeloid dendritic cell
Tissue
Blood
Developmental stage
Fifth decade stage
Adult stage
Disease
Visceral leishmaniasis
Hiv infectious disease
Sex
Male
Technology
10x 5' v1
Suspension type
Cell
Related Links
Zenodo record:10887674
ncbi.nlm.nih.gov
CELLxGENE
12,808 cells
•
Mimpen et al., 2025
Exploring cellular changes in ruptured human quadriceps tendons at single‐cell resolution
Explore
h5ad
Homo sapiens
Homo sapiens
Plasmacytoid dendritic cell
+21
Plasmacytoid dendritic cell
Tendon of quadriceps femoris
Tendon of quadriceps femoris
25-year-old stage
+5
25-year-old stage
Injury
+1
Injury
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Plasmacytoid dendritic cell
Natural killer cell
Dendritic cell
Osteoblast
T cell
Leukocyte
B cell
Neural cell
Pericyte
Endothelial cell of lymphatic vessel
Macrophage
Mononuclear phagocyte
Endothelial cell of vascular tree
Blood vessel smooth muscle cell
Endothelial cell of arteriole
Osteoclast
Adipocyte
Stromal cell
Granulocyte
Capillary endothelial cell
Fibroblast
Endothelial cell of venule
Tissue
Tendon of quadriceps femoris
Developmental stage
25-year-old stage
75-year-old stage
67-year-old stage
44-year-old stage
29-year-old stage
69-year-old stage
Disease
Injury
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
Github:Botnar-MSK-Atlas/quadriceps_tendon_atlas
HumanCellAtlas:8dcbd84a-6243-4501-a684-0dcd084bb536
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