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Cell
893
Nucleus
659
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Asap
43
Bgee
40
Cellxgene
2,077
Single cell portal
179
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Most cells
Fewest cells
2339
datasets
CELLxGENE
12,461 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Oligodendrocyte
+25
Oligodendrocyte
Hippocampal field
Hippocampal field
29-year-old stage
29-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
Hippocampal ca4 neuron
T cell
Medial ganglionic eminence derived interneuron
Pvalb chandelier gabaergic interneuron
Microglial cell
Oligodendrocyte precursor cell
B cell
Neuron
Ependymal cell
Pericyte
Committed oligodendrocyte precursor
Cerebral cortex neuron
Intratelencephalic-projecting glutamatergic cortical neuron
Vascular associated smooth muscle cell
Sst chodl gabaergic interneuron
Hippocampal ca1-3 neuron
Endothelial cell
Amygdala excitatory neuron
Caudal ganglionic eminence derived interneuron
Dentate gyrus granule cell
Central nervous system macrophage
Lamp5 lhx6 neuron
Near-projecting glutamatergic cortical neuron
Tissue
Hippocampal field
Developmental 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
12,444 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
+13
Kidney loop of henle thick ascending limb epithelial cell
Cortex of kidney
Cortex of kidney
56-year-old stage
56-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
Macula densa 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
Cortex of kidney
Developmental stage
56-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
12,376 cells
•
Zhang et al., 2023
A human embryonic limb cell atlas resolved in space and time
Explore
h5ad
Homo sapiens
Homo sapiens
Myoblast
+2
Myoblast
Forelimb
+1
Forelimb
10th week post-fertilization stage
+7
10th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 3' v2
+1
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Myoblast
Skeletal muscle myoblast
Muscle cell
Tissue
Forelimb
Hindlimb
Developmental stage
10th week post-fertilization stage
9th week post-fertilization stage
Carnegie stage 15
Carnegie stage 16
Carnegie stage 23
Carnegie stage 17
Carnegie stage 18
Carnegie stage 19
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
10x 5' v1
Suspension type
Cell
Related Links
Human Cell Atlas Developmental:embryonic-limb
ArrayExpress BioStudies:E-MTAB-10367
ArrayExpress BioStudies:E-MTAB-8813
Github:Peng-He-Lab/limbcellatlas
ArrayExpress BioStudies:E-MTAB-10514
Bgee
12,352 cells
•
Murat et al., 2022
The molecular evolution of spermatogenesis across mammals
Explore
scRNA-Seq droplet-based processed expression values per cell population in Pan troglodytes (tsv.gz)
scRNA-Seq droplet-based H5AD data per cell in Pan troglodytes (h5ad)
Pan troglodytes
Pan troglodytes
Sertoli cell
+7
Sertoli cell
Testis
Testis
Late adult stage
Late adult stage
Normal
Normal
Male
Male
10x genomics v2
10x genomics v2
Organism
Pan troglodytes
Cell type
Sertoli cell
Obsolete somatic cell
Late spermatid
Cell
Spermatocyte
Spermatogonium
Male germ line stem cell
Early spermatid
Tissue
Testis
Developmental stage
Late adult stage
Disease
Normal
Sex
Male
Technology
10x genomics v2
Suspension type
Related Links
ebi.ac.uk
CELLxGENE
12,351 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
+11
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 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
GEO series:GSE190094
Github:MacoskoLab/slideseq-tools
grekalab.org
Github:marshalljamie/Kidney-Slide-seq
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
CELLxGENE
12,330 cells
•
Escoubas et al., 2024
Type-I-interferon-responsive microglia shape cortical development and behavior
Explore
h5ad
Mus musculus
Mus musculus
Microglial cell
Microglial cell
Barrel cortex
Barrel cortex
5-day-old stage
+1
5-day-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Microglial cell
Tissue
Barrel cortex
Developmental stage
5-day-old stage
7-day-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
annamolofskylab.org
GEO series:GSE173173
lcdorman.shinyapps.io
CELLxGENE
12,295 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
T cell
+6
T cell
Mammary gland
Mammary gland
20-month-old stage and over
+2
20-month-old stage and over
Normal
Normal
Female
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Mus musculus
Cell type
T cell
B cell
Macrophage
Basal cell
Luminal epithelial cell of mammary gland
Stromal cell
Endothelial cell
Tissue
Mammary gland
Developmental stage
20-month-old stage and over
18-month-old stage
3-month-old stage
Disease
Normal
Sex
Female
Technology
10x 3' v2
Suspension type
Cell
Related Links
FigShare Dataset:Processed_files_to_use_with_scanpy_/8273102/2
CZ BioHub Portal:tabula-muris-senis
Github:czbiohub/tabula-muris-senis
GEO series:GSE132042
protocols.io:smartseq2-for-htp-generation-of-facs-sorted-single-2uwgexe
CELLxGENE
12,258 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
Hepatocyte
+10
Hepatocyte
Liver
Liver
31-year-old stage
31-year-old stage
Breast cancer
Breast cancer
Female
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Hepatocyte
Hepatic stellate cell
Endothelial cell of hepatic sinusoid
T cell
Neuron
Malignant cell
Mature nk t cell
Macrophage
Blood vessel smooth muscle cell
Blood vessel endothelial cell
Fibroblast
Tissue
Liver
Developmental stage
31-year-old stage
Disease
Breast cancer
Sex
Female
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
humantumoratlas.org
dbGaP Study:phs002371
CELLxGENE
12,205 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 adipose tissue
Subcutaneous adipose tissue
34-year-old stage
+3
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 adipose tissue
Developmental stage
34-year-old stage
24-year-old stage
33-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
12,162 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
Dendritic cell
+12
Dendritic cell
Ureter
Ureter
68-year-old stage
+8
68-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Dendritic cell
Central memory cd4-positive, alpha-beta t cell
Regulatory t cell
B cell
Non-classical monocyte
Classical monocyte
Double negative thymocyte
Mature nk t cell
Macrophage
Effector cd8-positive, alpha-beta t cell
Mast cell
Cd8-positive, alpha-beta memory t cell
Mucosal invariant t cell
Tissue
Ureter
Developmental stage
68-year-old stage
82-year-old stage
75-year-old stage
74-year-old stage
81-year-old stage
79-year-old stage
65-year-old stage
85-year-old stage
69-year-old stage
Disease
Normal
Sex
Female
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
12,132 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
+11
Kidney loop of henle thick ascending limb epithelial cell
Kidney
Kidney
6-month-old stage
6-month-old stage
Autosomal dominant polycystic kidney disease
Autosomal dominant polycystic 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 distal convoluted tubule epithelial cell
Tissue
Kidney
Developmental stage
6-month-old stage
Disease
Autosomal dominant polycystic kidney disease
Sex
Male
Technology
Slide-seqv2
Suspension type
Related Links
Github:marshalljamie/Kidney-Slide-seq
Github:MacoskoLab/slideseq-tools
grekalab.org
GEO series:GSE190094
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
CELLxGENE
12,118 cells
•
Easter et al., 2024
Single-cell and spatially resolved interactomics of tooth-associated keratinocytes in periodontitis
Explore
h5ad
Mus musculus
Mus musculus
Inflammatory cell
+7
Inflammatory cell
Gingiva
Gingiva
4-week-old stage
4-week-old stage
Normal
Normal
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Inflammatory cell
Glial cell
Muscle cell
Mural cell
Endothelial cell of vascular tree
Gingival epithelial cell
Fibroblast
Salivary gland cell
Tissue
Gingiva
Developmental stage
4-week-old stage
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE267511
Github:sequeira-science/Quinn_et_al_2024_NatComms_mousegingiva/tree/main
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