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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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Cell
896
Nucleus
659
Data Source
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Asap
43
Bgee
40
Cellxgene
2,080
Single cell portal
183
Sort
Most cells
Fewest cells
2346
datasets
CELLxGENE
4,494 cells
•
Oliver et al., 2024
Single-cell integration reveals metaplasia in inflammatory gut diseases
Explore
h5ad
Homo sapiens
Homo sapiens
Basal cell
+3
Basal cell
Gingiva
+2
Gingiva
37-year-old stage
+15
37-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Basal cell
Melanocyte
Epithelial cell
Keratinocyte
Tissue
Gingiva
Buccal mucosa
Periodontium
Developmental stage
37-year-old stage
21-year-old stage
61-year-old stage
39-year-old stage
28-year-old stage
51-year-old stage
57-year-old stage
24-year-old stage
23-year-old stage
35-year-old stage
Adult stage
32-year-old stage
33-year-old stage
31-year-old stage
22-year-old stage
Young adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
teichlab.org
ArrayExpress BioStudies:E-MTAB-14050
CELLxGENE
4,475 cells
•
Oliver et al., 2024
Single-cell integration reveals metaplasia in inflammatory gut diseases
Explore
h5ad
Homo sapiens
Homo sapiens
Intestine goblet cell
+6
Intestine goblet cell
Colon
Colon
19th week post-fertilization stage
+4
19th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 5' v2
+1
10x 5' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Intestine goblet cell
Best4+ enterocyte
Epithelial cell
Enteroendocrine cell
Intestinal crypt stem cell
Colonocyte
M cell of gut
Tissue
Colon
Developmental stage
19th week post-fertilization stage
15th week post-fertilization stage
17th week post-fertilization stage
12th week post-fertilization stage
16th week post-fertilization stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' v2
10x 3' v2
Suspension type
Cell
Related Links
teichlab.org
ArrayExpress BioStudies:E-MTAB-14050
CELLxGENE
4,454 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
T cell
+4
T cell
Skin of body
Skin of body
20-month-old stage and over
+1
20-month-old stage and over
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Mus musculus
Cell type
T cell
Stem cell of epidermis
Basal cell of epidermis
Epidermal cell
Keratinocyte stem cell
Tissue
Skin of body
Developmental stage
20-month-old stage and over
18-month-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
CZ BioHub Portal:tabula-muris-senis
protocols.io:smartseq2-for-htp-generation-of-facs-sorted-single-2uwgexe
Github:czbiohub/tabula-muris-senis
GEO series:GSE132042
FigShare Dataset:Processed_files_to_use_with_scanpy_/8273102/2
CELLxGENE
4,425 cells
•
De Simone et al., 2024
A comprehensive analysis framework for evaluating commercial single-cell RNA sequencing technologies
Explore
h5ad
Homo sapiens
Homo sapiens
Natural killer cell
+8
Natural killer cell
Blood
Blood
42-year-old stage
42-year-old stage
Normal
Normal
Male
Male
Asteria scrna-seq kit
Asteria scrna-seq kit
Cell
Cell
Organism
Homo sapiens
Cell type
Natural killer cell
Cytotoxic t cell
Plasmacytoid dendritic cell
Cd4-positive, alpha-beta t cell
Cd14-positive monocyte
Megakaryocyte
Cd14-low, cd16-positive monocyte
B cell
Dendritic cell
Tissue
Blood
Developmental stage
42-year-old stage
Disease
Normal
Sex
Male
Technology
Asteria scrna-seq kit
Suspension type
Cell
Related Links
Github:danledinh/scRNAseq-repo
ncbi.nlm.nih.gov
DOI:10.5281/zenodo.13910292
CELLxGENE
4,419 cells
•
Oliver et al., 2024
Single-cell integration reveals metaplasia in inflammatory gut diseases
Explore
h5ad
Homo sapiens
Homo sapiens
Best4+ enterocyte
+2
Best4+ enterocyte
Colon
Colon
Carnegie stage 19
+7
Carnegie stage 19
Normal
Normal
Female
+1
Female
10x 5' v2
+1
10x 5' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Best4+ enterocyte
Epithelial cell
Progenitor cell
Tissue
Colon
Developmental stage
Carnegie stage 19
12th week post-fertilization stage
9th week post-fertilization stage
10th week post-fertilization stage
Carnegie stage 17
Carnegie stage 22
Carnegie stage 18
11th week post-fertilization stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' v2
10x 3' v2
Suspension type
Cell
Related Links
teichlab.org
ArrayExpress BioStudies:E-MTAB-14050
Single Cell Portal
4,397 cells
Explore
Mus musculus
Mus musculus
Osteoblast
+6
Osteoblast
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Osteoblast
Stromal cell of bone marrow
Endothelial cell
Smooth muscle cell
Macrophage
Cell of skeletal muscle
Chondrocyte
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
CELLxGENE
4,355 cells
•
Xiang et al., 2020
A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell of lymphatic vessel
Endothelial cell of lymphatic vessel
Cervical lymph node
Cervical lymph node
Adult stage
Adult stage
Normal
Normal
Male
Male
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Endothelial cell of lymphatic vessel
Tissue
Cervical lymph node
Developmental stage
Adult stage
Disease
Normal
Sex
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
GEO series:GSE143877
med.stanford.edu
GEO series:GSE145121
igp.uu.se
CELLxGENE
4,335 cells
•
Voigt et al., 2019
Single-cell transcriptomics of the human retinal pigment epithelium and choroid in health and macular degeneration
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell
+9
Endothelial cell
Peripheral region of retina
+1
Peripheral region of retina
54-year-old stage
+2
54-year-old stage
Basal laminar drusen
+2
Basal laminar drusen
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Endothelial cell
Mature nk t cell
Retinal pigment epithelial cell
Mast cell
Schwann cell
Melanocyte
Macrophage
B cell
Pericyte
Fibroblast
Tissue
Peripheral region of retina
Fovea centralis
Developmental stage
54-year-old stage
82-year-old stage
79-year-old stage
Disease
Basal laminar drusen
Cataract
Age related macular degeneration 7
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
HumanCellAtlas:7880637a-35a1-4047-b422-b5eac2a2a358
GEO series:GSE135922
UCSC Cell Browser:retinal-pigment-epi
Single Cell Expression Atlas Experiment:E-GEOD-135922
CELLxGENE
4,333 cells
•
Guilliams et al., 2022
Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
Explore
h5ad
Homo sapiens
Homo sapiens
Neutrophil
+16
Neutrophil
Liver
Liver
68-year-old stage
+2
68-year-old stage
Normal
Normal
Female
+1
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Neutrophil
Hepatocyte
Endothelial cell of periportal hepatic sinusoid
Erythrocyte
Kupffer cell
Plasmacytoid dendritic cell
Hepatic stellate cell
Macrophage
Endothelial cell of pericentral hepatic sinusoid
Cholangiocyte
Plasma cell
B cell
Vascular associated smooth muscle cell
Basophil
Conventional dendritic cell
Fibroblast
Non-classical monocyte
Tissue
Liver
Developmental stage
68-year-old stage
58-year-old stage
59-year-old stage
Disease
Normal
Sex
Female
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
GEO series:GSE192742
livercellatlas.org
HumanCellAtlas:425c2759-db66-4c93-a358-a562c069b1f1
CELLxGENE
4,329 cells
•
Wang et al., 2019
Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine
Explore
h5ad
Homo sapiens
Homo sapiens
Stem cell
+6
Stem cell
Ascending colon
Ascending colon
54-year-old stage
+1
54-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Stem cell
Transit amplifying cell of colon
Paneth cell of colon
Colon goblet cell
Progenitor cell
Colonocyte
Enteroendocrine cell of colon
Tissue
Ascending colon
Developmental stage
54-year-old stage
67-year-old stage
Disease
Normal
Sex
Female
Male
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
4,328 cells
•
Gabitto et al., 2024
Integrated multimodal cell atlas of Alzheimer’s disease
Explore
h5ad
Homo sapiens
Homo sapiens
Vascular leptomeningeal cell
Vascular leptomeningeal cell
Middle temporal gyrus
Middle temporal gyrus
69-year-old stage
+21
69-year-old stage
Normal
+1
Normal
Female
+1
Female
10x multiome
+1
10x multiome
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Vascular leptomeningeal cell
Tissue
Middle temporal gyrus
Developmental stage
69-year-old stage
75-year-old stage
65-year-old stage
89-year-old stage
87-year-old stage
85-year-old stage
88-year-old stage
68-year-old stage
29-year-old stage
84-year-old stage
82-year-old stage
50-year-old stage
80-year-old stage
72-year-old stage
81-year-old stage
80 year-old and over stage
Adult stage
77-year-old stage
86-year-old stage
70-year-old stage
78-year-old stage
83-year-old stage
Disease
Normal
Dementia
Sex
Female
Male
Technology
10x multiome
10x 3' v3
Suspension type
Nucleus
Related Links
Alzheimer's Disease Research Center
Adult Changes in Thought Study
BRaIN-lab
Allen Brain Map:seattle-alzheimers-disease
AWS Open Data:allen-sea-ad-atlas
AD knowledge portal:syn26223298
CELLxGENE
4,289 cells
•
Bakken et al., 2021
Comparative cellular analysis of motor cortex in human, marmoset and mouse
Explore
h5ad
Callithrix jacchus
Callithrix jacchus
Oligodendrocyte precursor cell
+6
Oligodendrocyte precursor cell
Primary motor cortex
Primary motor cortex
Post-juvenile adult stage
Post-juvenile adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Callithrix jacchus
Cell type
Oligodendrocyte precursor cell
Endothelial cell
Oligodendrocyte
Microglial cell
Leptomeningeal cell
Pericyte
Astrocyte
Tissue
Primary motor cortex
Developmental stage
Post-juvenile adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
protocols.io:human-tissue-slicing-and-dissections-for-nuclear-i-dm6gpre85vzp
nemoanalytics.org
protocols.io:isolation-of-nuclei-from-adult-human-brain-tissue-eq2lyd1nqlx9/v2
Github:broadinstitute/Drop-seq
viewer.cytosplore.org
nemoanalytics.org
Github:AllenInstitute/BICCN_M1_Evo
Github:AllenInstitute/scrattch.hicat
NeMo archive:dat-ek5dbmu
protocols.io:extraction-of-nuclei-from-brain-tissue-2srged6
protocols.io:isolation-of-nuclei-from-adult-human-brain-tissue-j8nlk56k1l5r/v1
protocols.io:preparation-of-frozen-nuclei-for-single-nucleus-rn-eq2lyrdpgx9k/v1
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