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Cell Type
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Tissue
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Disease
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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
8,311 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
Tuft cell of large intestine
+6
Tuft cell of large intestine
Large intestine
Large intestine
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
Tuft cell of large intestine
Secretory cell
Enteroendocrine cell
Intestinal crypt stem cell
Large intestine goblet cell
Enterocyte of epithelium of large intestine
Epithelial cell of large intestine
Tissue
Large intestine
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
FigShare Dataset:Processed_files_to_use_with_scanpy_/8273102/2
CZ BioHub Portal:tabula-muris-senis
Github:czbiohub/tabula-muris-senis
protocols.io:smartseq2-for-htp-generation-of-facs-sorted-single-2uwgexe
Single Cell Portal
8,308 cells
•
Ziegler et al., 2020
SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues
Explore
Macaca mulatta
Macaca mulatta
T cell
+24
T cell
Disease
+1
Disease
Seq-well
Seq-well
Organism
Macaca mulatta
Cell type
T cell
Club cell
Endothelial cell
Mast cell
Pre-natural killer cell
Epithelial cell
Plasmacytoid dendritic cell
Enteroendocrine cell
Basophil mast progenitor cell
Goblet cell
Tuft cell
Pulmonary alveolar type 1 cell
Alveolar macrophage
Enterocyte
Plasma cell
Cd14-positive monocyte
Eosinophil
Ciliated epithelial cell
B cell
Epithelial fate stem cell
Fibroblast
Dendritic cell
Enterocyte of epithelium proper of large intestine
Pulmonary alveolar type 2 cell
Non-classical monocyte
Tissue
Developmental stage
Disease
Disease
Hiv infectious disease
Sex
Technology
Seq-well
Suspension type
Related Links
cellxgene.cziscience.com
cellxgene.cziscience.com
ASAP
8,304 cells
•
Li et al., 2022
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly
Explore
h5ad
Drosophila melanogaster
Drosophila melanogaster
Neuron
+13
Neuron
Haltere
Haltere
Day 5 of adulthood
Day 5 of adulthood
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Organism
Drosophila melanogaster
Cell type
Neuron
Fat cell
Tracheolar cell
Glial cell
Somatic precursor cell
Male germline cell
Hemocyte
Epithelial cell
Muscle cell
Adult glial cell
Sensory neuron
Oenocyte
Neuron
Female germline cell
Tissue
Haltere
Developmental stage
Day 5 of adulthood
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Related Links
ArrayExpress BioStudies:E-MTAB-10519
Single Cell Portal
8,268 cells
Explore
Mus musculus
Mus musculus
Pituitary gland cell
Pituitary gland cell
Normal
Normal
Mixed sex
Mixed sex
10x 3' v3
10x 3' v3
Organism
Mus musculus
Cell type
Pituitary gland cell
Tissue
Developmental stage
Disease
Normal
Sex
Mixed sex
Technology
10x 3' v3
Suspension type
CELLxGENE
8,263 cells
•
Oliver et al., 2024
Single-cell integration reveals metaplasia in inflammatory gut diseases
Explore
h5ad
Homo sapiens
Homo sapiens
Basal cell
+6
Basal cell
Parotid gland
+1
Parotid gland
34-year-old stage
+4
34-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Basal cell
Melanocyte
Ionocyte
Epithelial cell
Myoepithelial cell
Acinar cell of salivary gland
Salivary gland glandular cell
Tissue
Parotid gland
Labial gland
Developmental stage
34-year-old stage
26-year-old stage
68-year-old stage
28-year-old stage
24-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
teichlab.org
ArrayExpress BioStudies:E-MTAB-14050
CELLxGENE
8,242 cells
•
Bakken et al., 2021
Comparative cellular analysis of motor cortex in human, marmoset and mouse
Explore
h5ad
Mus musculus
Mus musculus
Glutamatergic neuron
Glutamatergic neuron
Primary motor cortex
Primary motor cortex
Prime adult stage
Prime adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Mus musculus
Cell type
Glutamatergic neuron
Tissue
Primary motor cortex
Developmental stage
Prime 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
CELLxGENE
8,213 cells
•
Johansen et al., 2023
Interindividual variation in human cortical cell type abundance and expression
Explore
h5ad
Homo sapiens
Homo sapiens
L6b glutamatergic cortical neuron
L6b glutamatergic cortical neuron
Neocortex
Neocortex
Adult stage
Adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
L6b glutamatergic cortical neuron
Tissue
Neocortex
Developmental stage
Adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
knowledge.brain-map.org
Allen Brain Map Atlases:rnaseq/human-mtg-10x_sea-ad
NeMo archive:dat-p3eei0g
Github:AllenInstitute/human_variation
Allen Brain Map:classes/multimodal-characterization
CELLxGENE
8,193 cells
•
Orozco et al., 2020
Integration of eQTL and a Single-Cell Atlas in the Human Eye Identifies Causal Genes for Age-Related Macular Degeneration
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+9
T cell
Retina
Retina
65-year-old stage
+3
65-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
T cell
Endothelial cell
Retinal pigment epithelial cell
Schwann cell
Melanocyte
Myeloid cell
B cell
Pericyte
Mueller cell
Astrocyte
Tissue
Retina
Developmental stage
65-year-old stage
77-year-old stage
70-year-old stage
79-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
GEO series:GSE135133
HumanCellAtlas:e090445c-6971-4212-bc5f-ae4ec3914102
BroadInstitute Single-Cell Portal:SCP484/nucseq-from-human-control-eyes-scrnaseq
Single Cell Portal
8,190 cells
Explore
Mus musculus
Mus musculus
Obsolete inhibitory neuron
+3
Obsolete inhibitory neuron
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Obsolete inhibitory neuron
Oligodendrocyte
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 (MD716) (section 40)
Corresponding registered brain section (MD716) (section 41)
Corresponding registered brain section (MD716) (section 42)
Corresponding registered brain section (MD716) (section 43)
Corresponding registered brain section (MD716) (section 44)
Corresponding registered brain section (MD716) (section 45)
CELLxGENE
8,172 cells
•
de Morree et al., 2025
A molecular cell atlas of mouse lemur, an emerging model primate
Explore
h5ad
Microcebus murinus
Microcebus murinus
T cell
+33
T cell
Pancreas
Pancreas
Post-juvenile adult stage
Post-juvenile adult stage
Normal
Normal
Female
+1
Female
Smart-seq2
+1
Smart-seq2
Cell
Cell
Organism
Microcebus murinus
Cell type
T cell
Neutrophil
Stromal cell
Natural killer cell
Endothelial cell of lymphatic vessel
Non-myelinating schwann cell
Reticular cell
Mature nk t cell
Cd8-positive, alpha-beta t cell
Pancreatic acinar cell
Pancreatic pp cell
Endothelial cell of artery
Capillary endothelial cell
Plasmacytoid dendritic cell
Pancreatic endocrine cell
Pancreatic a cell
Lymphocyte
Adipocyte
Macrophage
Pancreatic d cell
Plasma cell
Cd4-positive, alpha-beta t cell
Vein endothelial cell
Type b pancreatic cell
Mesothelial cell
B cell
Pericyte
Monocyte
Epithelial cell of exocrine pancreas
Vascular associated smooth muscle cell
Pancreatic ductal cell
Conventional dendritic cell
Fibroblast
Dendritic cell
Tissue
Pancreas
Developmental stage
Post-juvenile adult stage
Disease
Normal
Sex
Female
Male
Technology
Smart-seq2
10x 3' v2
Suspension type
Cell
Related Links
tabula-microcebus.sf.czbiohub.org
UCSC Cell Browser:tabula-microcebus
app.globus.org
CELLxGENE
8,168 cells
•
Leng et al., 2021
Molecular characterization of selectively vulnerable neurons in Alzheimer’s disease
Explore
h5ad
Homo sapiens
Homo sapiens
Oligodendrocyte
Oligodendrocyte
Entorhinal cortex
Entorhinal cortex
87-year-old stage
+7
87-year-old stage
Normal
+1
Normal
Male
Male
10x 3' v2
10x 3' v2
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Oligodendrocyte
Tissue
Entorhinal cortex
Developmental stage
87-year-old stage
71-year-old stage
82-year-old stage
50-year-old stage
72-year-old stage
80 year-old and over stage
77-year-old stage
60-year-old stage
Disease
Normal
Alzheimer disease
Sex
Male
Technology
10x 3' v2
Suspension type
Nucleus
Related Links
kampmannlab.ucsf.edu
GEO series:GSE147528
synapse.org:#!Synapse:syn21788402/wiki/601825
HumanCellAtlas:7dcffc32-7c82-4396-9a4f-88b5579bfe8a
CELLxGENE
8,166 cells
•
Bakken et al., 2021
Comparative cellular analysis of motor cortex in human, marmoset and mouse
Explore
h5ad
Callithrix jacchus
Callithrix jacchus
Glutamatergic neuron
Glutamatergic neuron
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
Glutamatergic neuron
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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