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Disease
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Technology
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Cell
934
Nucleus
679
Data Source
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ASAP
79
Bgee
40
CELLxGENE
2,213
Single Cell Portal
183
Sort
Most cells
Fewest cells
2515
datasets
CELLxGENE
25,660 cells
•
Pelka et al., 2021
Spatially organized multicellular immune hubs in human colorectal cancer
Explore
h5ad
Homo sapiens
Homo sapiens
Germinal center b cell
+1
Germinal center b cell
Colorectum
Colorectum
69-year-old stage
+34
69-year-old stage
Normal
+1
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Germinal center b cell
Mature b cell
Tissue
Colorectum
Developmental stage
69-year-old stage
91-year-old stage
42-year-old stage
89-year-old stage
71-year-old stage
53-year-old stage
61-year-old stage
52-year-old stage
48-year-old stage
56-year-old stage
55-year-old stage
84-year-old stage
82-year-old stage
50-year-old stage
90-year-old stage
51-year-old stage
57-year-old stage
72-year-old stage
81-year-old stage
49-year-old stage
35-year-old stage
58-year-old stage
59-year-old stage
67-year-old stage
77-year-old stage
64-year-old stage
45-year-old stage
62-year-old stage
70-year-old stage
60-year-old stage
78-year-old stage
36-year-old stage
47-year-old stage
76-year-old stage
73-year-old stage
Disease
Normal
Colon adenocarcinoma
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
Broad Institute Single Cell Portal
CRC Immune Hubs
GSE178341
dbGAP
HCA
CELLxGENE
25,642 cells
•
Krienen et al., 2023
A marmoset brain cell census reveals regional specialization of cellular identities
Explore
h5ad
Callithrix jacchus
Callithrix jacchus
Glutamatergic neuron
Glutamatergic neuron
Lateral amygdaloid nucleus
+2
Lateral amygdaloid nucleus
Prime adult stage
Prime adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Callithrix jacchus
Cell type
Glutamatergic neuron
Tissue
Lateral amygdaloid nucleus
Medial amygdaloid nucleus
Amygdala
Developmental stage
Prime adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
assets.nemoarchive.org
submit.brainimagelibrary.org
CELLxGENE
25,641 cells
•
Karakasheva et al., 2026
An Epigenetic Basis for Sustained Inflammatory Epithelial Progenitor Cell States in Crohn’s Disease
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell
+12
Endothelial cell
Right colon
Right colon
21-year-old stage
+7
21-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Endothelial cell
Mature nk t cell
Mast cell
Epithelial cell
Cd8-positive, alpha-beta memory t cell
Macrophage
Neuronal receptor cell
Plasma cell
Cd4-positive, alpha-beta memory t cell
B cell
Monocyte
Myofibroblast cell
Fibroblast
Tissue
Right colon
Developmental stage
21-year-old stage
52-year-old stage
38-year-old stage
55-year-old stage
50-year-old stage
51-year-old stage
58-year-old stage
18-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
GSE305528
CELLxGENE
25,593 cells
•
Yayon et al., 2024
A spatial human thymus cell atlas mapped to a continuous tissue axis
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+8
T cell
Thymus
Thymus
2-year-old stage
+5
2-year-old stage
Normal
Normal
Female
+1
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
T cell
Endothelial cell
Smooth muscle cell
Epithelial cell
Macrophage
Myelocyte
B cell
Fibroblast
Dendritic cell
Tissue
Thymus
Developmental stage
2-year-old stage
3-month-old stage
6-month-old stage
19-month-old stage
5-month-old stage
14-month-old stage
Disease
Normal
Sex
Female
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
github.com
BioImage Archive
PRJEB77091
EGAD00001015384
E-MTAB-8581
GSE271304
GSE206710
CITE-seq
TissueTag github
CELLxGENE
25,382 cells
•
Reed et al., 2024
A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast
Explore
h5ad
Homo sapiens
Homo sapiens
Natural killer cell
+13
Natural killer cell
Breast
Breast
37-year-old stage
+32
37-year-old stage
Normal
Normal
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Natural killer cell
Mature nk t cell
Cd4-positive helper t cell
Cd8-positive, alpha-beta memory t cell
Macrophage
Unswitched memory b cell
Tc1 cell
Innate lymphoid cell
Plasma cell
Naive thymus-derived cd4-positive, alpha-beta t cell
Naive b cell
Dendritic cell
Class switched memory b cell
Effector memory cd8-positive, alpha-beta t cell
Tissue
Breast
Developmental stage
37-year-old stage
21-year-old stage
34-year-old stage
65-year-old stage
53-year-old stage
52-year-old stage
48-year-old stage
30-year-old stage
39-year-old stage
29-year-old stage
38-year-old stage
56-year-old stage
55-year-old stage
28-year-old stage
57-year-old stage
24-year-old stage
23-year-old stage
35-year-old stage
58-year-old stage
59-year-old stage
25-year-old stage
33-year-old stage
45-year-old stage
62-year-old stage
41-year-old stage
46-year-old stage
31-year-old stage
36-year-old stage
19-year-old stage
63-year-old stage
20-year-old stage
27-year-old stage
40-year-old stage
Disease
Normal
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
trained CellTypist logistic regression models
github.com
E-MTAB-13664
CELLxGENE
25,339 cells
•
Gupta et al., 2023
Mapping the transcriptional landscape of human white and brown adipogenesis using single-nuclei RNA-seq
Explore
h5ad
Homo sapiens
Homo sapiens
Preadipocyte
+1
Preadipocyte
Preadipocyte
Preadipocyte
56-year-old stage
56-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Preadipocyte
White adipocyte
Tissue
Preadipocyte
Developmental stage
56-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
link.springer.com
phs002461
github.com
CELLxGENE
25,333 cells
•
de Morree et al., 2025
A molecular cell atlas of mouse lemur, an emerging model primate
Explore
h5ad
Microcebus murinus
Microcebus murinus
Natural killer cell
+12
Natural killer cell
Skin of body
Skin of body
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
Natural killer cell
Endothelial cell of lymphatic vessel
Endothelial cell
Cd8-positive, alpha-beta t cell
Endothelial cell of artery
Melanocyte
Basal cell of epidermis
Epithelial cell of sweat gland
Innate lymphoid cell
Hair follicle cell
Vein endothelial cell
Langerhans cell
Epidermal cell
Tissue
Skin of body
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
cells.ucsc.edu
Globus
ASAP
v8
25,333 cells
•
de Morree et al., 2025
A molecular cell atlas of mouse lemur, an emerging model primate
Explore
h5ad
Microcebus murinus
Microcebus murinus
Organism
Microcebus murinus
Cell type
Tissue
Developmental stage
Disease
Sex
Technology
Suspension type
CELLxGENE
25,281 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
Podocyte
+13
Podocyte
Kidney
Kidney
13-week-old stage
13-week-old stage
Normal
Normal
Male
Male
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Podocyte
Endothelial cell
Kidney interstitial fibroblast
Blood vessel smooth muscle cell
Kidney collecting duct intercalated cell
Leukocyte
Macrophage
Kidney distal convoluted tubule epithelial cell
Kidney granular cell
Kidney collecting duct principal cell
Kidney loop of henle thick ascending limb epithelial cell
Macula densa epithelial cell
Mesangial cell
Kidney proximal convoluted tubule epithelial cell
Tissue
Kidney
Developmental stage
13-week-old stage
Disease
Normal
Sex
Male
Technology
Slide-seqv2
Suspension type
Related Links
ncbi.nlm.nih.gov
Kidney Slide-seq Github
protocols.io
Macosko Lab Slide-seq Github
grekalab.org
CELLxGENE
25,186 cells
•
Joseph et al., 2020
Urethral luminal epithelia are castration‐insensitive cells of the proximal prostate
Explore
h5ad
Homo sapiens
Homo sapiens
Luminal cell of prostate epithelium
+4
Luminal cell of prostate epithelium
Transition zone of prostate
+1
Transition zone of prostate
29-year-old stage
+4
29-year-old stage
Benign prostatic hyperplasia
+1
Benign prostatic hyperplasia
Male
Male
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Luminal cell of prostate epithelium
Secretory cell
Neuroendocrine cell
Epithelial cell of urethra
Basal cell of prostate epithelium
Tissue
Transition zone of prostate
Peripheral zone of prostate
Developmental stage
29-year-old stage
57-year-old stage
72-year-old stage
74-year-old stage
31-year-old stage
Disease
Benign prostatic hyperplasia
Normal
Sex
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
strandlab.net
Human Raw Data
Mouse Raw Data
www.gudmap.org
CELLxGENE
25,166 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
Podocyte
+13
Podocyte
Cortex of kidney
Cortex of kidney
54-year-old stage
54-year-old stage
Normal
Normal
Male
Male
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
Podocyte
Endothelial cell
Kidney interstitial fibroblast
Blood vessel smooth muscle cell
Kidney collecting duct intercalated cell
Leukocyte
Macrophage
Kidney distal convoluted tubule epithelial cell
Kidney granular cell
Kidney collecting duct principal cell
Kidney loop of henle thick ascending limb epithelial cell
Macula densa epithelial cell
Mesangial cell
Kidney proximal convoluted tubule epithelial cell
Tissue
Cortex of kidney
Developmental stage
54-year-old stage
Disease
Normal
Sex
Male
Technology
Slide-seqv2
Suspension type
Related Links
ncbi.nlm.nih.gov
Kidney Slide-seq Github
protocols.io
Macosko Lab Slide-seq Github
grekalab.org
Single Cell Portal
25,136 cells
Explore
Mus musculus
Mus musculus
Neutrophil
+19
Neutrophil
Human papillomavirus-related squamous cell carcinoma
Human papillomavirus-related squamous cell carcinoma
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Neutrophil
Tissue-resident macrophage
Mature nk t cell
Suppressor macrophage
Inflammatory macrophage
Stem cell
Plasmacytoid dendritic cell
Basal cell of epidermis
Macrophage
Cd4-positive, cd25-positive, alpha-beta regulatory t cell
Cd4-positive, cd8-intermediate double-positive thymocyte
Macrophage dendritic cell progenitor
Activated cd8-positive, alpha-beta t cell
B cell
Monocyte
Elicited macrophage
Conventional dendritic cell
Fibroblast
Osteoclast
Dendritic cell
Tissue
Developmental stage
Disease
Human papillomavirus-related squamous cell carcinoma
Sex
Technology
10x 3' v2
Suspension type
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