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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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Technology
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Cell
893
Nucleus
659
Data Source
0
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Asap
43
Bgee
40
Cellxgene
2,077
Single cell portal
179
Sort
Most cells
Fewest cells
2339
datasets
CELLxGENE
3,834 cells
•
Pelka et al., 2021
Spatially organized multicellular immune hubs in human colorectal cancer
Explore
h5ad
Homo sapiens
Homo sapiens
Mast cell
Mast cell
Colorectum
Colorectum
62-year-old stage
+33
62-year-old stage
Normal
+1
Normal
Female
+1
Female
10x 3' v2
+1
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Mast cell
Tissue
Colorectum
Developmental stage
62-year-old stage
49-year-old stage
42-year-old stage
59-year-old stage
64-year-old stage
91-year-old stage
56-year-old stage
55-year-old stage
82-year-old stage
57-year-old stage
60-year-old stage
35-year-old stage
77-year-old stage
76-year-old stage
61-year-old stage
36-year-old stage
89-year-old stage
78-year-old stage
72-year-old stage
67-year-old stage
47-year-old stage
81-year-old stage
52-year-old stage
58-year-old stage
84-year-old stage
90-year-old stage
50-year-old stage
45-year-old stage
53-year-old stage
69-year-old stage
73-year-old stage
51-year-old stage
70-year-old stage
71-year-old stage
Disease
Normal
Colon adenocarcinoma
Sex
Female
Male
Technology
10x 3' v2
10x 3' v3
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
3,824 cells
•
Sampath Kumar et al., 2023
Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis
Explore
h5ad
Mus musculus
Mus musculus
Spinal cord interneuron
+11
Spinal cord interneuron
Embryo
Embryo
Theiler stage 14
Theiler stage 14
Normal
Normal
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Spinal cord interneuron
Neurectodermal cell
Gut endothelial cell
Hemangioblast
Cardiac valve cell
Endodermal cell
Primitive red blood cell
Midbrain dopaminergic neuron
Premigratory neural crest cell
Mesodermal cell
Neuroplacodal cell
Surface ectodermal cell
Tissue
Embryo
Developmental stage
Theiler stage 14
Disease
Normal
Sex
Technology
Slide-seqv2
Suspension type
Related Links
Chen Lab
figshare.com
FigShare Dataset:E8_5_Embryo2_h5ad/21695849/1
FigShare Dataset:E9_0_Embryo_h5ad/21695879/1
GEO series:GSE197353
CELLxGENE
3,799 cells
•
Leng et al., 2021
Molecular characterization of selectively vulnerable neurons in Alzheimer’s disease
Explore
h5ad
Homo sapiens
Homo sapiens
Mature microglial cell
Mature microglial cell
Superior frontal gyrus
Superior frontal gyrus
82-year-old stage
+7
82-year-old stage
Alzheimer disease
+1
Alzheimer disease
Male
Male
10x 3' v2
10x 3' v2
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Mature microglial cell
Tissue
Superior frontal gyrus
Developmental stage
82-year-old stage
60-year-old stage
77-year-old stage
72-year-old stage
80 year-old and over stage
87-year-old stage
50-year-old stage
71-year-old stage
Disease
Alzheimer disease
Normal
Sex
Male
Technology
10x 3' v2
Suspension type
Nucleus
Related Links
GEO series:GSE147528
kampmannlab.ucsf.edu
synapse.org:#!Synapse:syn21788402/wiki/601825
HumanCellAtlas:7dcffc32-7c82-4396-9a4f-88b5579bfe8a
CELLxGENE
3,799 cells
•
Litviňuková et al., 2020
Cells of the adult human heart
Explore
h5ad
Homo sapiens
Homo sapiens
Epicardial adipocyte
Epicardial adipocyte
Heart left ventricle
+5
Heart left ventricle
Seventh decade stage
+3
Seventh decade stage
Normal
Normal
Female
+1
Female
10x 3' v2
+1
10x 3' v2
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Epicardial adipocyte
Tissue
Heart left ventricle
Heart right ventricle
Left cardiac atrium
Interventricular septum
Apex of heart
Right cardiac atrium
Developmental stage
Seventh decade stage
Fifth decade stage
Sixth decade stage
Eighth decade stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
10x 3' v3
Suspension type
Nucleus
Related Links
UCSC Cell Browser:heart-cell-atlas
ENA Project:ERP123138
support.10xgenomics.com
UCSC Genome Browser:hgTrackUi?db=hg38&g=heartCellAtlas&position=default
Teichmann lab
Github:cartal/HCA_Heart
heartcellatlas.org
HumanCellAtlas:ad98d3cd-26fb-4ee3-99c9-8a2ab085e737
CELLxGENE
3,797 cells
•
Wang et al., 2019
Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine
Explore
h5ad
Homo sapiens
Homo sapiens
Colon goblet cell
+6
Colon goblet cell
Rectum
Rectum
66-year-old stage
+1
66-year-old stage
Normal
Normal
Female
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Colon goblet cell
Progenitor cell
Colonocyte
Stem cell
Transit amplifying cell of colon
Enteroendocrine cell of colon
Paneth cell of colon
Tissue
Rectum
Developmental stage
66-year-old stage
50-year-old stage
Disease
Normal
Sex
Female
Technology
10x 3' v2
Suspension type
Cell
Related Links
UCSC Cell Browser:human-intestine
GEO series:GSE125970
Single Cell Expression Atlas Experiment:E-GEOD-125970
CELLxGENE
3,764 cells
•
Isola et al., 2024
A single-cell atlas of the aging mouse ovary
Explore
h5ad
Mus musculus
Mus musculus
Oocyte
+2
Oocyte
Ovary
Ovary
9-month-old stage
+1
9-month-old stage
Normal
Normal
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Oocyte
Luteal cell
Granulosa cell
Tissue
Ovary
Developmental stage
9-month-old stage
3-month-old stage
Disease
Normal
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE232309
Github:StoutLab/OvarianAgingAtlas
omrf.shinyapps.io
CELLxGENE
3,760 cells
•
Sampath Kumar et al., 2023
Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis
Explore
h5ad
Mus musculus
Mus musculus
Notochordal cell
+15
Notochordal cell
Embryo
Embryo
Theiler stage 14
Theiler stage 14
Normal
Normal
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Notochordal cell
Spinal cord interneuron
Paraxial cell
Neurectodermal cell
Gut endothelial cell
Splanchnic mesodermal cell
Hemangioblast
Cardiac valve cell
Endodermal cell
Primitive red blood cell
Midbrain dopaminergic neuron
Anterior visceral endoderm cell
Premigratory neural crest cell
Mesodermal cell
Neuroplacodal cell
Surface ectodermal 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
3,755 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
Natural killer cell
+8
Natural killer cell
Subcutaneous adipose tissue
Subcutaneous adipose tissue
20-month-old stage and over
+2
20-month-old stage and over
Normal
Normal
Female
+1
Female
Smart-seq2
Smart-seq2
Cell
Cell
Organism
Mus musculus
Cell type
Natural killer cell
T cell
B cell
Cd4-positive, alpha-beta t cell
Cd8-positive, alpha-beta t cell
Endothelial cell
Epithelial cell
Mesenchymal stem cell of adipose tissue
Myeloid cell
Tissue
Subcutaneous adipose tissue
Developmental stage
20-month-old stage and over
18-month-old stage
3-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
3,749 cells
•
Sampath Kumar et al., 2023
Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis
Explore
h5ad
Mus musculus
Mus musculus
Spinal cord interneuron
+12
Spinal cord interneuron
Embryo
Embryo
Theiler stage 14
Theiler stage 14
Normal
Normal
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Spinal cord interneuron
Paraxial cell
Gut endothelial cell
Splanchnic mesodermal cell
Hemangioblast
Cardiac valve cell
Endodermal cell
Primitive red blood cell
Midbrain dopaminergic neuron
Premigratory neural crest cell
Mesodermal cell
Neuroplacodal cell
Surface ectodermal cell
Tissue
Embryo
Developmental stage
Theiler stage 14
Disease
Normal
Sex
Technology
Slide-seqv2
Suspension type
Related Links
figshare.com
FigShare Dataset:E8_5_Embryo2_h5ad/21695849/1
FigShare Dataset:E9_0_Embryo_h5ad/21695879/1
Chen Lab
GEO series:GSE197353
CELLxGENE
3,735 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
Basal cell of epidermis
+1
Basal cell of epidermis
Tongue
Tongue
20-month-old stage and over
+2
20-month-old stage and over
Normal
Normal
Female
+1
Female
Smart-seq2
Smart-seq2
Cell
Cell
Organism
Mus musculus
Cell type
Basal cell of epidermis
Keratinocyte
Tissue
Tongue
Developmental stage
20-month-old stage and over
18-month-old stage
3-month-old stage
Disease
Normal
Sex
Female
Male
Technology
Smart-seq2
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
3,726 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
Dendritic cell
+6
Dendritic cell
Blood
Blood
66-year-old stage
66-year-old stage
Covid-19
Covid-19
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Dendritic cell
B cell
Neutrophil
Platelet
Mature nk t cell
Plasma cell
Myeloid cell
Tissue
Blood
Developmental stage
66-year-old stage
Disease
Covid-19
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
Mendeley Data Dataset:fm7v43jrbk/2
Github:simslab/cluster_diffex2018
COVID-19 cell atlas
CELLxGENE
3,699 cells
•
Madissoon et al., 2022
A spatially resolved atlas of the human lung characterizes a gland-associated immune niche
Explore
h5ad
Homo sapiens
Homo sapiens
Naive b cell
+4
Naive b cell
Lung
+4
Lung
66-year-old stage
+8
66-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v2
+2
10x 3' v2
Cell
+1
Cell
Organism
Homo sapiens
Cell type
Naive b cell
Memory b cell
Iga plasma cell
Igg plasma cell
Plasmablast
Tissue
Lung
Trachea
Upper lobe of left lung
Lower lobe of left lung
Bronchus
Developmental stage
66-year-old stage
59-year-old stage
64-year-old stage
Seventh decade stage
75-year-old stage
35-year-old stage
Sixth decade stage
58-year-old stage
29-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
10x 5' transcription profiling
10x 3' v3
Suspension type
Cell
Nucleus
Related Links
ENA Project:PRJEB52292
ArrayExpress BioStudies:E-MTAB-11640
Bioimage Archive:S-BIAD570
Sanger Dataset:5locationslung
HumanCellAtlas:957261f7-2bd6-4358-a6ed-24ee080d5cfc
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