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890
Nucleus
655
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Asap
43
Bgee
40
Cellxgene
2,066
Single cell portal
179
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Most cells
Fewest cells
2328
datasets
CELLxGENE
57,855 cells
•
Johansen et al., 2023
Interindividual variation in human cortical cell type abundance and expression
Explore
h5ad
Homo sapiens
Homo sapiens
Oligodendrocyte
Oligodendrocyte
Neocortex
Neocortex
Adult stage
Adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Oligodendrocyte
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
Allen Brain Map:classes/multimodal-characterization
NeMo archive:dat-p3eei0g
Github:AllenInstitute/human_variation
CELLxGENE
57,723 cells
•
Chen et al., 2021
Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps
Explore
h5ad
Homo sapiens
Homo sapiens
Transit amplifying cell
+8
Transit amplifying cell
Hepatic flexure of colon
+6
Hepatic flexure of colon
66-year-old stage
+18
66-year-old stage
Hyperplastic polyp
+5
Hyperplastic polyp
Female
+1
Female
Trudrop
Trudrop
Cell
Cell
Organism
Homo sapiens
Cell type
Transit amplifying cell
Neoplastic cell
Abnormal cell
Tuft cell
Gut absorptive cell
Intestinal crypt stem cell of colon
Intestinal epithelial cell
Goblet cell
Intestinal enteroendocrine cell
Tissue
Hepatic flexure of colon
Rectum
Transverse colon
Sigmoid colon
Hepatic cecum
Descending colon
Ascending colon
Developmental stage
66-year-old stage
70-year-old stage
57-year-old stage
62-year-old stage
46-year-old stage
52-year-old stage
60-year-old stage
64-year-old stage
74-year-old stage
67-year-old stage
71-year-old stage
63-year-old stage
56-year-old stage
58-year-old stage
68-year-old stage
51-year-old stage
53-year-old stage
72-year-old stage
55-year-old stage
Disease
Hyperplastic polyp
Normal
Colorectal cancer
Tubular adenoma
Colon sessile serrated adenoma/polyp
Tubulovillous adenoma
Sex
Female
Male
Technology
Trudrop
Suspension type
Cell
Related Links
HumanCellAtlas:50154d1e-2308-44bf-9608-10c7afaa560b
humantumoratlas.org
dbGaP Study:phs002371
CELLxGENE
57,422 cells
•
van Zyl et al., 2022
Cell atlas of the human ocular anterior segment: Tissue-specific and shared cell types
Explore
h5ad
Homo sapiens
Homo sapiens
Schwann cell
+7
Schwann cell
Iris
Iris
66-year-old stage
+4
66-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Schwann cell
Smooth muscle cell of sphincter of pupil
Lymphocyte
Macrophage
Pigmented epithelial cell
Fibroblast
Blood vessel endothelial cell
Melanocyte
Tissue
Iris
Developmental stage
66-year-old stage
65-year-old stage
Adult stage
47-year-old stage
30-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
GEO series:GSE199013
HumanCellAtlas:16e99159-78bc-44aa-b479-55a5e903bf50
BroadInstitute Single-Cell Portal:SCP1841/cell-atlas-of-the-human-ocular-anterior-segment-tissue-specific-and-shared-cell-types
CELLxGENE
57,414 cells
•
Krienen et al., 2023
A marmoset brain cell census reveals regional specialization of cellular identities
Explore
h5ad
Callithrix jacchus
Callithrix jacchus
Microglial cell
Microglial cell
Putamen
+31
Putamen
Prime adult stage
+1
Prime adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Callithrix jacchus
Cell type
Microglial cell
Tissue
Putamen
Ventral thalamus
Cerebellum lobule
Posterior hypothalamic region
Secondary visual cortex
Hippocampal formation
Lateral geniculate body
Primary somatosensory cortex
Lateral nuclear group of thalamus
Brodmann (1909) area 23
Temporal cortex
Central amygdaloid nucleus
Dorsal thalamus
Medial amygdaloid nucleus
Primary auditory cortex
Dorsolateral prefrontal cortex
Thalamic complex
Temporal lobe
Brodmann (1909) area 25
Parietal cortex
Primary motor cortex
Amygdala
Primary visual cortex
Lateral amygdaloid nucleus
Anterior hypothalamic region
Ventral lateral nucleus of thalamus
Caudate nucleus
Medial dorsal nucleus of thalamus
Nucleus accumbens
Basal forebrain
Brainstem
Prefrontal cortex
Developmental stage
Prime adult stage
Late adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
NeMo archive:dat-1je0mn3
submit.brainimagelibrary.org
Single Cell Portal
57,056 cells
Explore
Mus musculus
Mus musculus
Astrocyte
+5
Astrocyte
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Astrocyte
Oligodendrocyte
Obsolete inhibitory neuron
Obsolete excitatory neuron
Microglial cell
Brain microvascular endothelial cell
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
Related Links
Corresponding registered brain section (MD721) (section 247)
Corresponding registered brain section (MD721) (section 248)
Corresponding registered brain section (MD721) (section 249)
Corresponding registered brain section (MD721) (section 250)
Corresponding registered brain section (MD721) (section 251)
Corresponding registered brain section (MD721) (section 252)
CELLxGENE
57,019 cells
•
Madissoon et al., 2019
scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell of lymphatic vessel
+19
Endothelial cell of lymphatic vessel
Lung parenchyma
Lung parenchyma
Eighth decade stage
+3
Eighth decade stage
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Endothelial cell of lymphatic vessel
Cd4-positive, alpha-beta t cell
Muscle cell
Mast cell
Monocyte
Mononuclear leukocyte
Lung multiciliated epithelial cell
Cd8-positive, alpha-beta cytotoxic t cell
Conventional dendritic cell
Fibroblast
Blood vessel endothelial cell
B cell
Lung macrophage
Dendritic cell
Plasma cell
Pulmonary alveolar epithelial cell
Regulatory t cell
T cell
Plasmacytoid dendritic cell
Natural killer cell
Tissue
Lung parenchyma
Developmental stage
Eighth decade stage
Fifth decade stage
Seventh decade stage
Sixth decade stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
protocols.io:cgap-macs-live-dead-separation-dm6gp71jgzpn/v1
tissuestabilitycellatlas.org
HumanCellAtlas:c4077b3c-5c98-4d26-a614-246d12c2e5d7
protocols.io:cgap-human-lung-dissociation-tissue-stability-stud-5jyl8noe7l2w/v1
Github:elo073/TissStab
ncbi.nlm.nih.gov
protocols.io:cgap-freezing-human-tissue-in-isopentane-n2bvjk1ngk5w/v1
Single Cell Expression Atlas Experiment:E-HCAD-1
UCSC Cell Browser:tissue-stability
protocols.io:cgap-human-spleen-dissociation-tissue-stability-st-ewov1yb92vr2/v1
protocols.io:cgap-human-oesophagus-epithelium-dissociation-tiss-eq2lydbxqlx9/v1
Bgee
56,902 cells
•
Davie et al., 2018
A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain
Explore
Bulk RNA-Seq processed expression values in Drosophila melanogaster (tsv.gz)
Drosophila melanogaster
Drosophila melanogaster
Adult antennal lobe projection neuron adpn
+59
Adult antennal lobe projection neuron adpn
Brain
Brain
Day 1 of adulthood
+7
Day 1 of adulthood
Normal
Normal
Mixed sex
Mixed sex
10x genomics v2
+1
10x genomics v2
Organism
Drosophila melanogaster
Cell type
Adult antennal lobe projection neuron adpn
Adult dopaminergic neuron
Medulla intrinsic neuron mi1
Medulla tangential neuron mt3
Adult ccap neuron
Proximal medullary amacrine neuron pm4
Distal medullary amacrine neuron dm9
Transmedullary neuron tm9
Adult mushroom body output neuron
Medulla tangential neuron mt2
Astrocyte-like glial cell
Photoreceptor cell
Adult myoinhibitory peptide neuron
Itp neuron
Lnv neuron
Peptidergic neuron
Distal medullary amacrine neuron
Pacemaker neuron
Adult kenyon cell
Centrifugal neuron c3
Adult brain cell body glial cell
Proximal medullary amacrine neuron
Adult peptidergic neuron
Adult optic chiasma glial cell
Transmedullary neuron
Lamina wide-field 1 neuron
Lamina monopolar neuron l3
Adult optic lobe neuron
Lamina monopolar neuron l1
Lamina monopolar neuron l2
Transmedullary neuron tm5
Adult gamma kenyon cell
Adult capability neuron
Adult brain perineurial glial cell
Transmedullary neuron tm5c
Medulla tangential neuron mt1
Adult neuron
Adult hugin neuron
Centrifugal neuron c2
Central nervous system neuron
Adult corazonin neuron
Adult dopaminergic pam neuron
Adult olfactory projection neuron
Lamina wide-field 2 neuron
Adult insulin secreting cell of pars intercerebralis
Proximal medullary amacrine neuron pm3
Obsolete neurosecretory neuron
Subperineurial glial cell
Adult plasmatocyte
Cchamide-1 neuron
Dn1 neuron
Adult tyraminergic neuron
Lamina monopolar neuron
Adult octopaminergic neuron
Transmedullary y neuron tmy14
Neural cell
Sugar-sensing neuron of the adult brain
Adult ensheathing glial cell
Medial antennal lobe tract projection neuron
Adult serotonergic neuron
Tissue
Brain
Developmental stage
Day 1 of adulthood
Day 3 of adulthood
Day 30 of adulthood
Day 15 of adulthood
Day 6 of adulthood
Day 50 of adulthood
Day 9 of adulthood
Day 0 of adulthood
Disease
Normal
Sex
Mixed sex
Technology
10x genomics v2
Illumina
Suspension type
Related Links
SRA Project:SRP125768
CELLxGENE
56,507 cells
•
Liang et al., 2023
A multi-omics atlas of the human retina at single-cell resolution
Explore
h5ad
Homo sapiens
Homo sapiens
Amacrine cell
Amacrine cell
Peripheral region of retina
+2
Peripheral region of retina
65-year-old stage
+4
65-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Amacrine cell
Tissue
Peripheral region of retina
Fovea centralis
Macula lutea proper
Developmental stage
65-year-old stage
78-year-old stage
73-year-old stage
84-year-old stage
83-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
UCSC Cell Browser:retina-atac
HumanCellAtlas:9c20a245-f2c0-43ae-82c9-2232ec6b594f
GEO series:GSE226108
CELLxGENE
56,367 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Astrocyte
+10
Astrocyte
Dentate gyrus of hippocampal formation
Dentate gyrus of hippocampal formation
50-year-old stage
+2
50-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Astrocyte
Oligodendrocyte precursor cell
Oligodendrocyte
Leukocyte
Vascular associated smooth muscle cell
Fibroblast
Ependymal cell
Pericyte
Endothelial cell
Neuron
Central nervous system macrophage
Tissue
Dentate gyrus of hippocampal formation
Developmental stage
50-year-old stage
42-year-old 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
55,968 cells
•
Gabitto et al., 2024
Integrated multimodal cell atlas of Alzheimer’s disease
Explore
h5ad
Homo sapiens
Homo sapiens
Lamp5 gabaergic interneuron
Lamp5 gabaergic interneuron
Dorsolateral prefrontal cortex
Dorsolateral prefrontal cortex
80-year-old stage
+20
80-year-old stage
Normal
+1
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Lamp5 gabaergic interneuron
Tissue
Dorsolateral prefrontal cortex
Developmental stage
80-year-old stage
85-year-old stage
82-year-old stage
70-year-old stage
77-year-old stage
50-year-old stage
86-year-old stage
80 year-old and over stage
89-year-old stage
75-year-old stage
78-year-old stage
68-year-old stage
42-year-old stage
72-year-old stage
88-year-old stage
84-year-old stage
69-year-old stage
29-year-old stage
87-year-old stage
81-year-old stage
83-year-old stage
Disease
Normal
Dementia
Sex
Female
Male
Technology
10x 3' v3
10x multiome
Suspension type
Nucleus
Related Links
Alzheimer's Disease Research Center
Adult Changes in Thought Study
BRaIN-lab
AD knowledge portal:syn26223298
AWS Open Data:allen-sea-ad-atlas
Allen Brain Map:seattle-alzheimers-disease
CELLxGENE
55,515 cells
•
Chiou et al., 2023
A single-cell multi-omic atlas spanning the adult rhesus macaque brain
Explore
h5ad
Macaca mulatta
Macaca mulatta
Oligodendrocyte precursor cell
Oligodendrocyte precursor cell
Cerebellar vermis
+26
Cerebellar vermis
Prime adult stage
+1
Prime adult stage
Normal
Normal
Female
+1
Female
Sci-rna-seq3
Sci-rna-seq3
Nucleus
Nucleus
Organism
Macaca mulatta
Cell type
Oligodendrocyte precursor cell
Tissue
Cerebellar vermis
Entorhinal cortex
Brodmann (1909) area 19
Inferior temporal gyrus
Hippocampal formation
Cerebrocerebellum
Lateral geniculate body
Primary somatosensory cortex
Perirhinal cortex
Corpus callosum
Anterior cingulate cortex
Primary auditory cortex
Dorsolateral prefrontal cortex
Pons
Primary motor cortex
Superior temporal sulcus
Midbrain
Amygdala
Primary visual cortex
Superior parietal cortex
Medulla oblongata
Inferior parietal cortex
Ventral lateral nucleus of thalamus
Medial dorsal nucleus of thalamus
Nucleus accumbens
Head of caudate nucleus
Prefrontal cortex
Developmental stage
Prime adult stage
Juvenile stage
Disease
Normal
Sex
Female
Male
Technology
Sci-rna-seq3
Suspension type
Nucleus
Related Links
NeMo archive:dat-rtmm5q2
Zenodo record:7925943
Zenodo record:7925933
Zenodo record:7925925
DOI:10.17504/protocols.io.9yih7ue
CELLxGENE
55,348 cells
•
Jin et al., 2021
An interactive single cell web portal identifies gene and cell networks in COVID-19 host responses
Explore
h5ad
Homo sapiens
Homo sapiens
Classical monocyte
Classical monocyte
Blood
Blood
82-year-old stage
+32
82-year-old stage
Normal
+1
Normal
Female
+1
Female
10x 3' v3
+2
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Classical monocyte
Tissue
Blood
Developmental stage
82-year-old stage
70-year-old stage
Fourth decade stage
62-year-old stage
46-year-old stage
60-year-old stage
80 year-old and over stage
48-year-old stage
67-year-old stage
Eighth decade stage
75-year-old stage
27-year-old stage
37-year-old stage
Adult stage
78-year-old stage
36-year-old stage
63-year-old stage
59-year-old stage
54-year-old stage
Fifth decade stage
47-year-old stage
68-year-old stage
61-year-old stage
49-year-old stage
53-year-old stage
73-year-old stage
Seventh decade stage
84-year-old stage
39-year-old stage
Third decade stage
29-year-old stage
38-year-old stage
Sixth decade stage
Disease
Normal
Covid-19
Sex
Female
Male
Technology
10x 3' v3
Seq-well
10x 3' v2
Suspension type
Cell
Related Links
cincinnatichildrens.org
toppcell.cchmc.org
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