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Cell
871
Nucleus
653
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Asap
43
Bgee
40
Cellxgene
2,045
Single cell portal
176
Sort
Most cells
Fewest cells
2304
datasets
Single Cell Portal
710,704 cells
•
Fiskin et al., 2023
Multi-modal skin atlas identifies a multicellular immune-stromal community associated with altered cornification and specific T cell expansion in atopic dermatitis
Explore
Homo sapiens
Homo sapiens
Iga plasma cell
+26
Iga plasma cell
Atopic eczema
+1
Atopic eczema
10x 3' v3
10x 3' v3
Organism
Homo sapiens
Cell type
Iga plasma cell
Innate lymphoid cell
Plasmablast
Schwann cell
Keratinocyte
Mast cell
Igg plasma cell
Vein endothelial cell
Hair follicular keratinocyte
Smooth muscle cell
Melanocyte
Neutrophil
Dendritic cell
Gamma-delta t cell
Regulatory t cell
Sweat secreting cell
Capillary endothelial cell
Pericyte
Sebaceous gland cell
Skin fibroblast
Cd8-positive, alpha-beta t cell
Endothelial cell of lymphatic vessel
Natural killer cell
Macrophage
T cell
Naive b cell
Endothelial cell of artery
Tissue
Developmental stage
Disease
Atopic eczema
Normal
Sex
Technology
10x 3' v3
Suspension type
CELLxGENE
709,372 cells
•
Velmeshev et al., 2023
Single-cell analysis of prenatal and postnatal human cortical development
Explore
h5ad
Homo sapiens
Homo sapiens
Astrocyte
+4
Astrocyte
Primary motor cortex
+9
Primary motor cortex
54-year-old stage
+39
54-year-old stage
Normal
Normal
Female
+1
Female
10x multiome
+2
10x multiome
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Astrocyte
Oligodendrocyte precursor cell
Oligodendrocyte
Neural cell
Microglial cell
Tissue
Primary motor cortex
Caudal ganglionic eminence
Cerebral cortex
Ganglionic eminence
Temporal cortex
Insular cortex
Lateral ganglionic eminence
Cingulate cortex
Frontal cortex
Medial ganglionic eminence
Developmental stage
54-year-old stage
39-year-old stage
Ninth lmp month stage
53-year-old stage
19-year-old stage
21-year-old stage
Infant stage
13-year-old stage
Newborn stage (0-28 days)
1-month-old stage
17-year-old stage
1-year-old stage
4-year-old stage
6-year-old stage
40-year-old stage
12-year-old stage
45-year-old stage
3-year-old stage
10-year-old stage
2-month-old stage
3-month-old stage
14-year-old stage
2-year-old stage
22-year-old stage
15-year-old stage
Fifth lmp month stage
Seventh lmp month stage
Fourth lmp month stage
5-month-old stage
28-year-old stage
4-month-old stage
5-year-old stage
8-year-old stage
25-year-old stage
20-year-old stage
Sixth lmp month stage
44-year-old stage
34-year-old stage
16-year-old stage
Eighth lmp month stage
Disease
Normal
Sex
Female
Male
Technology
10x multiome
10x 3' v3
10x 3' v2
Suspension type
Nucleus
Related Links
Github:velmeshevlab/dev_hum_cortex
Zenodo record:7245297
pre-postnatal-cortex.cells.ucsc.edu
NeMo archive:dat-3ah9h9x
CELLxGENE
704,296 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Fibroblast
+11
Fibroblast
Heart left ventricle
+7
Heart left ventricle
Third decade stage
+4
Third decade stage
Normal
Normal
Female
+1
Female
10x multiome
+2
10x multiome
Cell
+1
Cell
Organism
Homo sapiens
Cell type
Fibroblast
Regular atrial cardiac myocyte
Myeloid cell
Mast cell
Regular ventricular cardiac myocyte
Mural cell
Lymphocyte
Neural cell
Adipocyte
Endothelial cell of lymphatic vessel
Mesothelial cell
Endothelial cell
Tissue
Heart left ventricle
Apex of heart
Left cardiac atrium
Interventricular septum
Right cardiac atrium
Sinoatrial node
Heart right ventricle
Atrioventricular node
Developmental stage
Third decade stage
Sixth decade stage
Eighth decade stage
Fifth decade stage
Seventh decade stage
Disease
Normal
Sex
Female
Male
Technology
10x multiome
10x 3' v3
10x 3' v2
Suspension type
Cell
Nucleus
Related Links
heartcellatlas.org
ArrayExpress BioStudies:E-MTAB-12916
ArrayExpress BioStudies:E-MTAB-12919
ArrayExpress BioStudies:E-MTAB-12975
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
CELLxGENE
693,682 cells
•
Lee et al., 2024
Single-cell atlas of transcriptomic vulnerability across multiple neurodegenerative and neuropsychiatric diseases
Explore
h5ad
Homo sapiens
Homo sapiens
L6b glutamatergic neuron of the primary motor cortex
+24
L6b glutamatergic neuron of the primary motor cortex
Dorsolateral prefrontal cortex
Dorsolateral prefrontal cortex
54-year-old stage
+27
54-year-old stage
Lewy body dementia
+10
Lewy body dementia
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
L6b glutamatergic neuron of the primary motor cortex
Astrocyte
Lamp5 gabaergic interneuron
L6 intratelencephalic projecting glutamatergic neuron
Gabaergic neuron
Smooth muscle cell
L2/3 intratelencephalic projecting glutamatergic neuron
Vip gabaergic interneuron
Oligodendrocyte precursor cell
L2/3-6 intratelencephalic projecting glutamatergic neuron
Plasma cell
Oligodendrocyte
B cell
L6 corticothalamic-projecting glutamatergic cortical neuron
Pericyte
L5/6 near-projecting glutamatergic neuron
Pvalb gabaergic interneuron
Natural killer cell
Sst gabaergic interneuron
Perivascular macrophage
L5 extratelencephalic projecting glutamatergic cortical neuron
Vascular leptomeningeal cell
Microglial cell
T cell
Endothelial cell
Tissue
Dorsolateral prefrontal cortex
Developmental stage
54-year-old stage
78-year-old stage
80 year-old and over stage
73-year-old stage
74-year-old stage
72-year-old stage
83-year-old stage
85-year-old stage
81-year-old stage
82-year-old stage
86-year-old stage
70-year-old stage
75-year-old stage
79-year-old stage
89-year-old stage
64-year-old stage
68-year-old stage
66-year-old stage
77-year-old stage
69-year-old stage
76-year-old stage
88-year-old stage
87-year-old stage
80-year-old stage
84-year-old stage
67-year-old stage
65-year-old stage
71-year-old stage
Disease
Lewy body dementia
Diabetes mellitus
Dementia
Amyotrophic lateral sclerosis
Parkinson disease
Head injury
Vascular dementia
Tauopathy
Normal
Alzheimer disease
Frontotemporal dementia
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
Github:DiseaseNeuroGenomics/PsychADxD
adknowledgeportal.synapse.org
psych-ad.org
DOI:10.1101/2024.11.06.24316592
DOI:10.1101/2024.11.01.24316586
DOI:10.1101/2024.11.02.24316590
DOI:10.1101/2024.11.04.24316495
DOI:10.1101/2025.01.29.635498
DOI:10.1101/2023.05.19.541376
DOI:10.1038/s41597-025-04687-5
DOI:10.1101/2024.11.01.24316589
DOI:10.1101/2023.03.17.533005
CELLxGENE
691,008 cells
•
Li et al., 2023
Integrated multi-omics single cell atlas of the human retina
Explore
h5ad
Homo sapiens
Homo sapiens
Offx cell
+12
Offx cell
Peripheral region of retina
+3
Peripheral region of retina
62-year-old stage
+53
62-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Offx cell
Invaginating midget bipolar cell
Retinal bipolar neuron
Diffuse bipolar 3b cell
Diffuse bipolar 4 cell
Diffuse bipolar 3a cell
Diffuse bipolar 6 cell
Giant bipolar cell
On-blue cone bipolar cell
Rod bipolar cell
Flat midget bipolar cell
Diffuse bipolar 1 cell
Diffuse bipolar 2 cell
Tissue
Peripheral region of retina
Fovea centralis
Macula lutea proper
Macula lutea
Developmental stage
62-year-old stage
27-year-old stage
78-year-old stage
80 year-old and over stage
73-year-old stage
74-year-old stage
72-year-old stage
53-year-old stage
21-year-old stage
83-year-old stage
85-year-old stage
81-year-old stage
82-year-old stage
17-year-old stage
52-year-old stage
86-year-old stage
70-year-old stage
41-year-old stage
Eighth decade stage
3-year-old stage
30-year-old stage
10-year-old stage
58-year-old stage
75-year-old stage
90 year-old and over stage
15-year-old stage
18-year-old stage
50-year-old stage
64-year-old stage
68-year-old stage
66-year-old stage
77-year-old stage
11-year-old stage
Late adult stage
69-year-old stage
32-year-old stage
76-year-old stage
88-year-old stage
63-year-old stage
60-year-old stage
80-year-old stage
Prime adult stage
84-year-old stage
25-year-old stage
46-year-old stage
24-year-old stage
67-year-old stage
43-year-old stage
60-79 year-old stage
65-year-old stage
71-year-old stage
34-year-old stage
16-year-old stage
47-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
Github:RCHENLAB/HRCA_reproducibility
CELLxGENE
685,024 cells
Explore
h5ad
Homo sapiens
Homo sapiens
Innate lymphoid cell
+24
Innate lymphoid cell
Blood
Blood
20-year-old stage
20-year-old stage
Normal
Normal
Male
Male
Scalebio single cell rna sequencing
Scalebio single cell rna sequencing
Cell
Cell
Organism
Homo sapiens
Cell type
Innate lymphoid cell
Plasmablast
Effector memory cd4-positive, alpha-beta t cell
Double negative thymocyte
Mucosal invariant t cell
Effector memory cd8-positive, alpha-beta t cell
Cd14-low, cd16-positive monocyte
Cd14-positive monocyte
Hematopoietic precursor cell
Central memory cd4-positive, alpha-beta t cell
Cd141-positive myeloid dendritic cell
Memory b cell
B cell
Gamma-delta t cell
Regulatory t cell
Cd1c-positive myeloid dendritic cell
Naive thymus-derived cd4-positive, alpha-beta t cell
Naive thymus-derived cd8-positive, alpha-beta t cell
Plasmacytoid dendritic cell
Cd16-negative, cd56-bright natural killer cell, human
Central memory cd8-positive, alpha-beta t cell
Natural killer cell
Platelet
Cd4-positive, alpha-beta t cell
Naive b cell
Tissue
Blood
Developmental stage
20-year-old stage
Disease
Normal
Sex
Male
Technology
Scalebio single cell rna sequencing
Suspension type
Cell
CELLxGENE
677,256 cells
•
Marshall et al., 2022
High-resolution Slide-seqV2 spatial transcriptomics enables discovery of disease-specific cell neighborhoods and pathways
Explore
h5ad
Homo sapiens
Homo sapiens
Kidney loop of henle thick ascending limb epithelial cell
+13
Kidney loop of henle thick ascending limb epithelial cell
Cortex of kidney
+1
Cortex of kidney
54-year-old stage
+7
54-year-old stage
Normal
Normal
Female
+1
Female
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
Kidney loop of henle thick ascending limb epithelial cell
Kidney proximal convoluted tubule epithelial cell
Kidney granular cell
Podocyte
Kidney interstitial fibroblast
Leukocyte
Kidney distal convoluted tubule epithelial cell
Mesangial cell
Blood vessel smooth muscle cell
Macrophage
Kidney collecting duct intercalated cell
Macula densa epithelial cell
Kidney collecting duct principal cell
Endothelial cell
Tissue
Cortex of kidney
Renal medulla
Developmental stage
54-year-old stage
62-year-old stage
72-year-old stage
53-year-old stage
50-year-old stage
64-year-old stage
56-year-old stage
65-year-old stage
Disease
Normal
Sex
Female
Male
Technology
Slide-seqv2
Suspension type
Related Links
GEO series:GSE190094
Github:marshalljamie/Kidney-Slide-seq
Github:MacoskoLab/slideseq-tools
grekalab.org
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
CELLxGENE
676,845 cells
•
Xu et al., 2023
Automatic cell-type harmonization and integration across Human Cell Atlas datasets
Explore
h5ad
Homo sapiens
Homo sapiens
Mature microglial cell
+14
Mature microglial cell
Hippocampal formation
Hippocampal formation
54-year-old stage
+12
54-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Mature microglial cell
Oligodendrocyte precursor cell
Oligodendrocyte
Vascular associated smooth muscle cell
Pericyte
Smooth muscle cell of the brain vasculature
Ependymal cell
Macrophage
Hippocampal pyramidal neuron
Vascular leptomeningeal cell
Hippocampal interneuron
T cell
Hippocampal astrocyte
Endothelial cell
Hippocampal granule cell
Tissue
Hippocampal formation
Developmental stage
54-year-old stage
26-year-old stage
42-year-old stage
48-year-old stage
40-year-old stage
50-year-old stage
51-year-old stage
79-year-old stage
29-year-old stage
60-year-old stage
37-year-old stage
24-year-old stage
44-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Nucleus
Related Links
ebi.ac.uk
EGA dataset:EGAD00001008575
celltypist.org
Github:ventolab/CVID
teichlab.org
CELLxGENE
670,749 cells
•
Barnes et al., 2023
Early human lung immune cell development and its role in epithelial cell fate
Explore
h5ad
Homo sapiens
Homo sapiens
Fibroblast
+47
Fibroblast
Lung
Lung
Carnegie stage 19
+18
Carnegie stage 19
Normal
Normal
Female
+1
Female
10x 5' transcription profiling
+2
10x 5' transcription profiling
Cell
Cell
Organism
Homo sapiens
Cell type
Fibroblast
Alveolar type 1 fibroblast cell
Innate lymphoid cell
Lung pericyte
Group 3 innate lymphoid cell, human
Common myeloid progenitor
Hematopoietic multipotent progenitor cell
Cd16-positive, cd56-dim natural killer cell, human
Mast cell
Large pre-b-ii cell
Cd14-low, cd16-positive monocyte
Group 2 innate lymphoid cell
Granulocyte
Early lymphoid progenitor
Cd14-positive monocyte
Fraction a pre-pro b cell
Smooth muscle cell
Lung secretory cell
Neutrophil
Pro-b cell
Epithelial cell of distal tubule
Early pro-b cell
Immature b cell
Dendritic cell
Regulatory t cell
Megakaryocyte
Late pro-b cell
Precursor b cell
Plasmacytoid dendritic cell
Erythroid lineage cell
Alveolar adventitial fibroblast
Cd8-positive, alpha-beta t cell
Megakaryocyte-erythroid progenitor cell
Cd16-negative, cd56-bright natural killer cell, human
Granulocyte monocyte progenitor cell
Natural killer cell
Macrophage
Mature b cell
Group 1 innate lymphoid cell
Pro-t cell
Myelocyte
Conventional dendritic cell
Ciliated cell
Monocyte
Cd4-positive, alpha-beta t cell
Megakaryocyte progenitor cell
Cd22-positive, cd38-low small pre-b cell
Endothelial cell
Tissue
Lung
Developmental stage
Carnegie stage 19
21st week post-fertilization stage
Carnegie stage 20
14th week post-fertilization stage
10th week post-fertilization stage
Carnegie stage 23
16th week post-fertilization stage
Carnegie stage 22
Carnegie stage 13
20th week post-fertilization stage
15th week post-fertilization stage
11th week post-fertilization stage
13th week post-fertilization stage
12th week post-fertilization stage
22nd week post-fertilization stage
18th week post-fertilization stage
9th week post-fertilization stage
17th week post-fertilization stage
Carnegie stage 16
Disease
Normal
Sex
Female
Male
Technology
10x 5' transcription profiling
10x 5' v1
10x 3' v2
Suspension type
Cell
Related Links
fetal-lung-immune.cellgeni.sanger.ac.uk
ArrayExpress BioStudies:E-MTAB-11528
Github:Peng-He-Lab/lung-immune-cell-atlas
Single Cell Portal
666,948 cells
Explore
Homo sapiens
Homo sapiens
Myeloid cell
+7
Myeloid cell
Glioblastoma
Glioblastoma
10x 5' v3
10x 5' v3
Organism
Homo sapiens
Cell type
Myeloid cell
Astrocyte
Malignant cell
Oligodendrocyte
Pericyte
Lymphocyte
Neuron
Endothelial cell
Tissue
Developmental stage
Disease
Glioblastoma
Sex
Technology
10x 5' v3
Suspension type
CELLxGENE
647,366 cells
•
Stephenson et al., 2021
Single-cell multi-omics analysis of the immune response in COVID-19
Explore
h5ad
Homo sapiens
Homo sapiens
Cd34-positive, cd38-negative hematopoietic stem cell
+45
Cd34-positive, cd38-negative hematopoietic stem cell
Blood
Blood
54-year-old stage
+45
54-year-old stage
Respiratory system disorder
+2
Respiratory system disorder
Female
+1
Female
10x 3' transcription profiling
10x 3' transcription profiling
Cell
Cell
Organism
Homo sapiens
Cell type
Cd34-positive, cd38-negative hematopoietic stem cell
Iga plasma cell
Plasmablast
Effector memory cd4-positive, alpha-beta t cell
Class switched memory b cell
Mucosal invariant t cell
Cd16-positive, cd56-dim natural killer cell, human
Igg plasma cell
Effector memory cd8-positive, alpha-beta t cell
Unswitched memory b cell
Dendritic cell, human
Cd14-low, cd16-positive monocyte
T-helper 22 cell
Myeloid lineage restricted progenitor cell
Cd14-positive monocyte
Group 2 innate lymphoid cell, human
Myeloid dendritic cell
Hematopoietic precursor cell
Central memory cd4-positive, alpha-beta t cell
Malignant cell
Immature b cell
T-helper 1 cell
Dendritic cell
B cell
Gamma-delta t cell
Regulatory t cell
T-helper 17 cell
Megakaryocyte
Naive thymus-derived cd4-positive, alpha-beta t cell
T-helper 2 cell
Naive thymus-derived cd8-positive, alpha-beta t cell
Plasmacytoid dendritic cell
Igm plasma cell
Cd8-positive, alpha-beta t cell
Ilc1, human
Effector cd8-positive, alpha-beta t cell
Cd16-negative, cd56-bright natural killer cell, human
Natural killer cell
Erythroid progenitor cell, mammalian
Platelet
Erythrocyte
Monocyte
Mature nk t cell
Cd4-positive, alpha-beta t cell
Naive b cell
T follicular helper cell
Tissue
Blood
Developmental stage
54-year-old stage
39-year-old stage
62-year-old stage
73-year-old stage
26-year-old stage
Ninth decade stage
Third decade stage
21-year-old stage
83-year-old stage
57-year-old stage
Sixth decade stage
49-year-old stage
Fourth decade stage
52-year-old stage
70-year-old stage
40-year-old stage
38-year-old stage
59-year-old stage
Eighth decade stage
30-year-old stage
55-year-old stage
58-year-old stage
50-year-old stage
51-year-old stage
64-year-old stage
68-year-old stage
66-year-old stage
77-year-old stage
69-year-old stage
76-year-old stage
Fifth decade stage
31-year-old stage
87-year-old stage
63-year-old stage
60-year-old stage
80-year-old stage
84-year-old stage
25-year-old stage
56-year-old stage
46-year-old stage
92-year-old stage
65-year-old stage
71-year-old stage
Seventh decade stage
44-year-old stage
47-year-old stage
Disease
Respiratory system disorder
Covid-19
Normal
Sex
Female
Male
Technology
10x 3' transcription profiling
Suspension type
Cell
Related Links
Github:scCOVID-19/COVIDPBMC
haniffalab.com
ArrayExpress BioStudies:E-MTAB-10026
UCSC Cell Browser:covid19-pbmc
EGA Study:EGAS00001005465
HumanCellAtlas:b963bd4b-4bc1-4404-8425-69d74bc636b8
CELLxGENE
638,941 cells
•
Jorstad et al., 2023
Transcriptomic cytoarchitecture reveals principles of human neocortex organization
Explore
h5ad
Homo sapiens
Homo sapiens
L2/3-6 intratelencephalic projecting glutamatergic neuron
L2/3-6 intratelencephalic projecting glutamatergic neuron
Primary motor cortex
+7
Primary motor cortex
Sixth decade stage
+5
Sixth decade stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
L2/3-6 intratelencephalic projecting glutamatergic neuron
Tissue
Primary motor cortex
Primary visual cortex
Dorsolateral prefrontal cortex
Primary somatosensory cortex
Primary auditory cortex
Middle temporal gyrus
Anterior cingulate cortex
Angular gyrus
Developmental stage
Sixth decade stage
42-year-old stage
50-year-old stage
29-year-old stage
60-year-old stage
43-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
Github:AllenInstitute/human_cross_areal
NeMo archive:dat-rg2rc5m
Allen Brain Map Atlases:rnaseq/human-multiple-cortical-areas-smart-seq
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