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Cell Type
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Tissue
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Developmental Stage
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Disease
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Sex
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Technology
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Suspension Type
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Cell
896
Nucleus
659
Data Source
0
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Asap
43
Bgee
40
Cellxgene
2,080
Single cell portal
183
Sort
Most cells
Fewest cells
2346
datasets
CELLxGENE
2,988 cells
•
Vinsland et al., 2025
Organotypic Timelapse recording with Transcriptomic Readout (OTTR) links cell behaviour to cell identity in human tissues
Explore
h5ad
Homo sapiens
Homo sapiens
Glioblast
+4
Glioblast
Telencephalon
Telencephalon
10th week post-fertilization stage
10th week post-fertilization stage
Normal
Normal
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Glioblast
Glutamatergic neuron
Forebrain neuroblast
Astrocyte
Gabaergic neuron
Tissue
Telencephalon
Developmental stage
10th week post-fertilization stage
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:linnarsson-lab/OTTR
Single Cell Portal
2,986 cells
Explore
Mus musculus musculus
Mus musculus musculus
T cell
+12
T cell
Normal
Normal
10x 3' v1
10x 3' v1
Organism
Mus musculus musculus
Cell type
T cell
Cell
Erythroid progenitor cell
Paneth cell
Epithelial cell
Plasmacytoid dendritic cell
Enteroendocrine cell
Goblet cell
Tuft cell
Enterocyte
B cell
Professional antigen presenting cell
Fibroblast
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v1
Suspension type
CELLxGENE
2,958 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
T cell
+8
T cell
Liver
Liver
55-year-old stage
55-year-old stage
Breast cancer
Breast cancer
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
T cell
Hepatocyte
Endothelial cell
Mature nk t cell
Macrophage
Malignant cell
B cell
Monocyte
Fibroblast
Tissue
Liver
Developmental stage
55-year-old stage
Disease
Breast cancer
Sex
Female
Technology
Slide-seqv2
Suspension type
Related Links
humantumoratlas.org
dbGaP Study:phs002371
CELLxGENE
2,951 cells
•
Chan et al., 2021
Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer
Explore
h5ad
Homo sapiens
Homo sapiens
Neutrophil
+3
Neutrophil
Pleural effusion
+5
Pleural effusion
69-year-old stage
+13
69-year-old stage
Small cell lung carcinoma
Small cell lung carcinoma
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Neutrophil
Classical monocyte
Plasmacytoid dendritic cell
Conventional dendritic cell
Tissue
Pleural effusion
Lung
Axilla
Liver
Adrenal gland
Lymph node
Developmental stage
69-year-old stage
75-year-old stage
71-year-old stage
68-year-old stage
55-year-old stage
72-year-old stage
81-year-old stage
74-year-old stage
67-year-old stage
77-year-old stage
64-year-old stage
62-year-old stage
70-year-old stage
47-year-old stage
Disease
Small cell lung carcinoma
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
data.humantumoratlas.org
dbGaP Study:phs002371
Single Cell Portal
2,947 cells
Explore
Mus musculus
Mus musculus
Obsolete inhibitory neuron
+4
Obsolete inhibitory neuron
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Obsolete inhibitory neuron
Oligodendrocyte precursor cell
Oligodendrocyte
Obsolete excitatory neuron
Astrocyte
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
Related Links
Corresponding registered brain section (MD704) (section 425)
CELLxGENE
2,923 cells
•
Yayon et al., 2024
A spatial human thymus cell atlas mapped to a continuous tissue axis
Explore
h5ad
Homo sapiens
Homo sapiens
Plasmacytoid dendritic cell
+2
Plasmacytoid dendritic cell
Thymus
Thymus
13th week post-fertilization stage
+13
13th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 5' v2
+3
10x 5' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Plasmacytoid dendritic cell
Macrophage
Conventional dendritic cell
Tissue
Thymus
Developmental stage
13th week post-fertilization stage
2-year-old stage
3-month-old stage
14th week post-fertilization stage
15th week post-fertilization stage
17th week post-fertilization stage
12th week post-fertilization stage
6-month-old stage
18th week post-fertilization stage
10-month-old stage
2-month-old stage
Newborn stage (0-28 days)
5-month-old stage
14-month-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' v2
10x 5' v1
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
Bioimage Archive:S-BIAD1257
ENA Project:PRJEB77091
EGA dataset:EGAD00001015384
ebi.ac.uk
GEO series:GSE271304
GEO series:GSE206710
ccgg.ugent.be
Github:Teichlab/TissueTag
Github:Teichlab/thymus_spatial_atlas/tree/main
Single Cell Portal
2,901 cells
Explore
Mus musculus
Mus musculus
Obsolete inhibitory neuron
+6
Obsolete inhibitory neuron
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Obsolete inhibitory neuron
Oligodendrocyte precursor cell
Oligodendrocyte
Astrocyte of the cerebellum
Microglial cell
Brain microvascular endothelial cell
Obsolete excitatory neuron
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
Related Links
Corresponding registered brain section (MD703) (section 584)
CELLxGENE
2,872 cells
•
Sampath Kumar et al., 2023
Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis
Explore
h5ad
Mus musculus
Mus musculus
Cardiac valve cell
+15
Cardiac valve cell
Embryo
Embryo
Theiler stage 14
Theiler stage 14
Normal
Normal
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Cardiac valve cell
Spinal cord interneuron
Premigratory neural crest cell
Paraxial cell
Notochordal cell
Neuroplacodal cell
Neurectodermal cell
Hemangioblast
Mesodermal cell
Gut endothelial cell
Primitive red blood cell
Splanchnic mesodermal cell
Surface ectodermal cell
Midbrain dopaminergic neuron
Endodermal cell
Anterior visceral endoderm cell
Tissue
Embryo
Developmental stage
Theiler stage 14
Disease
Normal
Sex
Technology
Slide-seqv2
Suspension type
Related Links
Chen Lab
GEO series:GSE197353
figshare.com
FigShare Dataset:E9_0_Embryo_h5ad/21695879/1
FigShare Dataset:E8_5_Embryo2_h5ad/21695849/1
CELLxGENE
2,868 cells
•
Yan et al., 2020
Cell Atlas of The Human Fovea and Peripheral Retina
Explore
h5ad
Homo sapiens
Homo sapiens
Retina horizontal cell
Retina horizontal cell
Peripheral region of retina
+1
Peripheral region of retina
69-year-old stage
+6
69-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Retina horizontal cell
Tissue
Peripheral region of retina
Fovea centralis
Developmental stage
69-year-old stage
65-year-old stage
53-year-old stage
74-year-old stage
64-year-old stage
60-year-old stage
78-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
GEO series:GSE148077
HumanCellAtlas:30dc3964-1135-4b56-b393-ce2dcbc6e379
BroadInstitute Single-Cell Portal:SCP839/cell-atlas-of-the-human-fovea-and-peripheral-retina
CELLxGENE
2,859 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
Endothelial cell of hepatic sinusoid
+10
Endothelial cell of hepatic sinusoid
Liver
Liver
3-month-old stage
+2
3-month-old stage
Normal
Normal
Female
+1
Female
Smart-seq2
Smart-seq2
Cell
Cell
Organism
Mus musculus
Cell type
Endothelial cell of hepatic sinusoid
T cell
Neutrophil
Hepatocyte
Natural killer cell
Kupffer cell
Mature nk t cell
Cd8-positive, alpha-beta t cell
Cd4-positive, alpha-beta t cell
B cell
Myeloid leukocyte
Tissue
Liver
Developmental stage
3-month-old stage
20-month-old stage and over
18-month-old stage
Disease
Normal
Sex
Female
Male
Technology
Smart-seq2
Suspension type
Cell
Related Links
GEO series:GSE132042
CZ BioHub Portal:tabula-muris-senis
protocols.io:smartseq2-for-htp-generation-of-facs-sorted-single-2uwgexe
Github:czbiohub/tabula-muris-senis
FigShare Dataset:Processed_files_to_use_with_scanpy_/8273102/2
CELLxGENE
2,834 cells
•
Szabo et al., 2021
Longitudinal profiling of respiratory and systemic immune responses reveals myeloid cell-driven lung inflammation in severe COVID-19
Explore
h5ad
Homo sapiens
Homo sapiens
Neutrophil
+5
Neutrophil
Respiratory airway
Respiratory airway
74-year-old stage
74-year-old stage
Covid-19
Covid-19
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Neutrophil
Mature nk t cell
Ionocyte
Epithelial cell
Myeloid cell
B cell
Tissue
Respiratory airway
Developmental stage
74-year-old stage
Disease
Covid-19
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:simslab/cluster_diffex2018
COVID-19 cell atlas
Mendeley Data Dataset:fm7v43jrbk/2
CELLxGENE
2,833 cells
•
Fawkner-Corbett et al., 2021
Spatiotemporal analysis of human intestinal development at single-cell resolution
Explore
h5ad
Homo sapiens
Homo sapiens
Mesothelial cell
+1
Mesothelial cell
Ileum
+1
Ileum
19th week post-fertilization stage
+9
19th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Mesothelial cell
Myofibroblast cell
Tissue
Ileum
Colon
Developmental stage
19th week post-fertilization stage
21st week post-fertilization stage
23rd week post-fertilization stage
13th week post-fertilization stage
14th week post-fertilization stage
17th week post-fertilization stage
16th week post-fertilization stage
18th week post-fertilization stage
Carnegie stage 22
11th week post-fertilization stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE158328
simmonslab.shinyapps.io
Mendeley Data Dataset:gncg57p5x9/2
dropbox.com
HumanCellAtlas:fa3f460f-4fb9-4ced-b548-8ba6a8ecae3f
GEO series:GSE158702
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