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Technology
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Cell
893
Nucleus
659
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Asap
43
Bgee
40
Cellxgene
2,077
Single cell portal
179
Sort
Most cells
Fewest cells
2339
datasets
CELLxGENE
11,127 cells
•
Andrews et al., 2024
Single-cell, single-nucleus, and spatial transcriptomics characterization of the immunological landscape in the healthy and PSC human liver
Explore
h5ad
Homo sapiens
Homo sapiens
Kupffer cell
+5
Kupffer cell
Caudate lobe of liver
Caudate lobe of liver
Young adult stage
+2
Young adult stage
Normal
Normal
Female
+1
Female
10x 3' v2
+1
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Kupffer cell
Classical monocyte
Monocyte
Macrophage
Liver dendritic cell
Myeloid cell
Tissue
Caudate lobe of liver
Developmental stage
Young adult stage
Prime adult stage
Late adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
10x 5' v1
Suspension type
Cell
Related Links
nature.com
GEO series:GSE240429
GEO series:GSE115469
GEO series:GSE243977
GEO series:GSE247128
GEO series:GSE245620
CELLxGENE
11,103 cells
•
Moerkens et al., 2024
An iPSC-derived small intestine-on-chip with self-organizing epithelial, mesenchymal, and neural cells
Explore
h5ad
Homo sapiens
Homo sapiens
Goblet cell
+7
Goblet cell
Intestinal mucosa
Intestinal mucosa
26-year-old stage
+1
26-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Goblet cell
Neuron
Enterocyte
Transit amplifying cell
Paneth cell
Myofibroblast cell
Enteroendocrine cell
Mesenchymal stem cell
Tissue
Intestinal mucosa
Developmental stage
26-year-old stage
29-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:umcg-immunogenetics/Intestine_on_Chip_Moerkens_2024
CELLxGENE
11,094 cells
•
Duran et al., 2025
A statistical framework for inferring genetic requirements from embryo-scale single-cell sequencing experiments
Explore
h5ad
Danio rerio
Danio rerio
Neuron
+1
Neuron
Cranial ganglion
+5
Cranial ganglion
Segmentation:14-19 somites
+9
Segmentation:14-19 somites
Normal
Normal
Sci-rna-seq3
Sci-rna-seq3
Nucleus
Nucleus
Organism
Danio rerio
Cell type
Neuron
Rohon-beard neuron
Tissue
Cranial ganglion
Lateral line ganglion
Epibranchial ganglion
Trigeminal ganglion
Vestibulocochlear ganglion
Spinal cord
Developmental stage
Segmentation:14-19 somites
Hatching:pec-fin
Larval:protruding-mouth
Pharyngula:prim-5
Pharyngula:high-pec
Hatching:long-pec
Segmentation:20-25 somites
Segmentation:26+ somites
Pharyngula:prim-15
Pharyngula:prim-25
Disease
Normal
Sex
Technology
Sci-rna-seq3
Suspension type
Nucleus
Related Links
GEO series:GSE295164
cole-trapnelllab.github.io
DOI:10.1038/s41586-023-06720-2
CELLxGENE
11,074 cells
•
Klughammer et al., 2024
A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features
Explore
h5ad
Homo sapiens
Homo sapiens
Monocyte
+3
Monocyte
Liver
Liver
54-year-old stage
54-year-old stage
Breast cancer
Breast cancer
Female
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Monocyte
Malignant cell
Macrophage
Fibroblast
Tissue
Liver
Developmental stage
54-year-old stage
Disease
Breast cancer
Sex
Female
Technology
10x 3' v2
Suspension type
Cell
Related Links
humantumoratlas.org
dbGaP Study:phs002371
CELLxGENE
11,031 cells
•
Marshall et al., 2022
High-resolution Slide-seqV2 spatial transcriptomics enables discovery of disease-specific cell neighborhoods and pathways
Explore
h5ad
Mus musculus
Mus musculus
Kidney loop of henle thick ascending limb epithelial cell
+12
Kidney loop of henle thick ascending limb epithelial cell
Kidney
Kidney
6-month-old stage
6-month-old stage
Autosomal dominant polycystic kidney disease
Autosomal dominant polycystic kidney disease
Male
Male
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Kidney loop of henle thick ascending limb epithelial cell
Kidney interstitial fibroblast
Leukocyte
Kidney proximal convoluted tubule epithelial cell
Podocyte
Kidney collecting duct principal cell
Macrophage
Blood vessel smooth muscle cell
Endothelial cell
Kidney collecting duct intercalated cell
Mesangial cell
Kidney granular cell
Kidney distal convoluted tubule epithelial cell
Tissue
Kidney
Developmental stage
6-month-old stage
Disease
Autosomal dominant polycystic kidney disease
Sex
Male
Technology
Slide-seqv2
Suspension type
Related Links
GEO series:GSE190094
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
Github:MacoskoLab/slideseq-tools
grekalab.org
Github:marshalljamie/Kidney-Slide-seq
CELLxGENE
11,005 cells
•
Marshall et al., 2022
High-resolution Slide-seqV2 spatial transcriptomics enables discovery of disease-specific cell neighborhoods and pathways
Explore
h5ad
Mus musculus
Mus musculus
Kidney loop of henle thick ascending limb epithelial cell
+11
Kidney loop of henle thick ascending limb epithelial cell
Kidney
Kidney
6-month-old stage
6-month-old stage
Autosomal dominant polycystic kidney disease
Autosomal dominant polycystic kidney disease
Male
Male
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Kidney loop of henle thick ascending limb epithelial cell
Kidney interstitial fibroblast
Leukocyte
Kidney proximal convoluted tubule epithelial cell
Podocyte
Kidney collecting duct principal cell
Macrophage
Blood vessel smooth muscle cell
Endothelial cell
Kidney collecting duct intercalated cell
Mesangial cell
Kidney distal convoluted tubule epithelial cell
Tissue
Kidney
Developmental stage
6-month-old stage
Disease
Autosomal dominant polycystic kidney disease
Sex
Male
Technology
Slide-seqv2
Suspension type
Related Links
Github:marshalljamie/Kidney-Slide-seq
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
Github:MacoskoLab/slideseq-tools
grekalab.org
GEO series:GSE190094
CELLxGENE
10,993 cells
•
Garcia-Alonso et al., 2022
Single-cell roadmap of human gonadal development
Explore
h5ad
Homo sapiens
Homo sapiens
Oocyte
+4
Oocyte
Gonad
Gonad
10th week post-fertilization stage
+15
10th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 5' v2
+1
10x 5' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Oocyte
Male germ cell
Germ cell
Primordial germ cell
Oogonial cell
Tissue
Gonad
Developmental stage
10th week post-fertilization stage
14th week post-fertilization stage
9th week post-fertilization stage
16th week post-fertilization stage
11th week post-fertilization stage
21st week post-fertilization stage
15th week post-fertilization stage
Carnegie stage 23
Carnegie stage 17
19th week post-fertilization stage
Carnegie stage 18
Carnegie stage 19
13th week post-fertilization stage
12th week post-fertilization stage
18th week post-fertilization stage
17th week post-fertilization stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' v2
10x 5' v1
Suspension type
Cell
Related Links
ArrayExpress BioStudies:E-MTAB-10551
ArrayExpress BioStudies:E-MTAB-11480
reproductivecellatlas.org
ventolab.org
CELLxGENE
10,980 cells
•
Bakken et al., 2021
Comparative cellular analysis of motor cortex in human, marmoset and mouse
Explore
h5ad
Homo sapiens
Homo sapiens
Gabaergic neuron
Gabaergic neuron
Primary motor cortex
Primary motor cortex
60-year-old stage
+1
60-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Gabaergic neuron
Tissue
Primary motor cortex
Developmental stage
60-year-old stage
50-year-old 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
10,957 cells
•
Klughammer et al., 2024
A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+6
T cell
Axilla
Axilla
38-year-old stage
38-year-old stage
Breast cancer
Breast cancer
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
T cell
Monocyte
Malignant cell
Macrophage
Endothelial cell
Fibroblast
Mast cell
Tissue
Axilla
Developmental stage
38-year-old stage
Disease
Breast cancer
Sex
Female
Technology
Slide-seqv2
Suspension type
Related Links
humantumoratlas.org
dbGaP Study:phs002371
CELLxGENE
10,946 cells
•
Chen et al., 2025
Determinants of sensitivity to HER2-targeted antibody drug conjugates in urothelial cancer
Explore
h5ad
Homo sapiens
Homo sapiens
Neoplastic cell
Neoplastic cell
Urinary bladder
Urinary bladder
Adult stage
Adult stage
Urinary bladder cancer
Urinary bladder cancer
Male
Male
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Neoplastic cell
Tissue
Urinary bladder
Developmental stage
Adult stage
Disease
Urinary bladder cancer
Sex
Male
Technology
10x 3' v3
Suspension type
Cell
CELLxGENE
10,937 cells
•
Gong et al., 2025
Multi-omic profiling reveals age-related immune dynamics in healthy adults
Explore
h5ad
Homo sapiens
Homo sapiens
Common myeloid progenitor
+4
Common myeloid progenitor
Blood
Blood
62-year-old stage
+24
62-year-old stage
Normal
+1
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Common myeloid progenitor
Platelet
Erythrocyte
Basophil mast progenitor cell
Common lymphoid progenitor
Tissue
Blood
Developmental stage
62-year-old stage
32-year-old stage
31-year-old stage
34-year-old stage
30-year-old stage
59-year-old stage
64-year-old stage
25-year-old stage
56-year-old stage
55-year-old stage
11-year-old stage
57-year-old stage
28-year-old stage
33-year-old stage
60-year-old stage
35-year-old stage
63-year-old stage
61-year-old stage
26-year-old stage
27-year-old stage
36-year-old stage
12-year-old stage
58-year-old stage
65-year-old stage
29-year-old stage
Disease
Normal
Cytomegalovirus infection
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
apps.allenimmunology.org
Github:aifimmunology/aifi-healthy-pbmc-reference
CELLxGENE collection:e9360edf-b0b7-4e01-bce8-e596814f13e7
dbGaP Study:phs003841
GEO series:GSE275067
CELLxGENE
10,928 cells
•
Gabitto et al., 2024
Integrated multimodal cell atlas of Alzheimer’s disease
Explore
h5ad
Homo sapiens
Homo sapiens
Pvalb chandelier gabaergic interneuron
Pvalb chandelier gabaergic interneuron
Middle temporal gyrus
Middle temporal gyrus
43-year-old stage
+23
43-year-old stage
Dementia
+1
Dementia
Female
+1
Female
10x multiome
+1
10x multiome
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Pvalb chandelier gabaergic interneuron
Tissue
Middle temporal gyrus
Developmental stage
43-year-old stage
68-year-old stage
88-year-old stage
86-year-old stage
82-year-old stage
83-year-old stage
60-year-old stage
75-year-old stage
80-year-old stage
77-year-old stage
Adult stage
89-year-old stage
78-year-old stage
72-year-old stage
80 year-old and over stage
81-year-old stage
87-year-old stage
84-year-old stage
65-year-old stage
85-year-old stage
50-year-old stage
29-year-old stage
69-year-old stage
70-year-old stage
Disease
Dementia
Normal
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
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