Home
Data
Contribute
Stats
Resources
Metadata schema
Tools
Community
About
Contact us
Organism
0
Clear
Cell Type
0
Clear
Tissue
0
Clear
Developmental Stage
0
Clear
Disease
0
Clear
Sex
0
Clear
Technology
0
Clear
Suspension Type
0
Clear
Cell
890
Nucleus
655
Data Source
0
Clear
Asap
43
Bgee
40
Cellxgene
2,066
Single cell portal
179
Sort
Most cells
Fewest cells
2328
datasets
CELLxGENE
36,299 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
Normal
Normal
Male
Male
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Kidney loop of henle thick ascending limb epithelial cell
Leukocyte
Macrophage
Kidney distal convoluted tubule epithelial cell
Kidney interstitial fibroblast
Kidney collecting duct principal cell
Blood vessel smooth muscle cell
Kidney collecting duct intercalated cell
Podocyte
Endothelial cell
Mesangial cell
Kidney proximal convoluted tubule epithelial cell
Tissue
Kidney
Developmental stage
6-month-old stage
Disease
Normal
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
36,191 cells
•
Ham et al., 2025
Single-nuclei sequencing of skeletal muscle reveals subsynaptic-specific transcripts involved in neuromuscular junction maintenance
Explore
h5ad
Mus musculus
Mus musculus
Myotendinous junction nucleus
+15
Myotendinous junction nucleus
Gastrocnemius
+1
Gastrocnemius
Prime adult stage
Prime adult stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Mus musculus
Cell type
Myotendinous junction nucleus
Schwann cell
Macrophage
Skeletal muscle satellite stem cell
Perineurial cell
Adipocyte
Tendon cell
Type iia muscle cell
Fibro/adipogenic progenitor cell
Blood vessel endothelial cell
Type iib muscle cell
Pericyte
Type iix muscle cell
Smooth muscle cell
Neuromuscular junction nucleus
Microvascular endothelial cell
Tissue
Gastrocnemius
Skeletal muscle tissue of tibialis anterior
Developmental stage
Prime adult stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
ruegglab.shinyapps.io
GEO series:GSE267910
CELLxGENE
35,987 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
+14
Kidney loop of henle thick ascending limb epithelial cell
Renal medulla
Renal medulla
62-year-old stage
62-year-old stage
Normal
Normal
Male
Male
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
Kidney loop of henle thick ascending limb epithelial cell
Kidney connecting tubule epithelial cell
Leukocyte
Kidney distal convoluted tubule epithelial cell
Kidney interstitial fibroblast
Kidney collecting duct principal cell
Kidney loop of henle thin descending limb epithelial cell
Blood vessel smooth muscle cell
Kidney collecting duct intercalated cell
Podocyte
Pericyte
Endothelial cell
Kidney loop of henle epithelial cell
Mesangial cell
Kidney proximal convoluted tubule epithelial cell
Tissue
Renal medulla
Developmental stage
62-year-old stage
Disease
Normal
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
35,959 cells
•
de Morree et al., 2025
A molecular cell atlas of mouse lemur, an emerging model primate
Explore
h5ad
Microcebus murinus
Microcebus murinus
Osteoblast
+27
Osteoblast
Bone marrow
Bone marrow
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
Osteoblast
Erythroid progenitor cell
Megakaryocyte progenitor cell
Cd4-positive, alpha-beta t cell
Pulmonary alveolar type 2 cell
Endothelial cell of sinusoid
Lymphocyte
Macrophage
Granulocyte monocyte progenitor cell
Erythroid lineage cell
Adipocyte
Neutrophil
Monocyte
Preosteoblast
Conventional dendritic cell
Fibroblast
Hematopoietic precursor cell
B cell
Cd8-positive, alpha-beta t cell
Dendritic cell
Plasma cell
Mature nk t cell
T cell
Plasmacytoid dendritic cell
Basophil
Eosinophil
Natural killer cell
Myeloid cell
Tissue
Bone marrow
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
35,957 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
Myofibroblast cell
+12
Myofibroblast cell
Right colon
Right colon
16-year-old stage
+7
16-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Myofibroblast cell
Cd4-positive, alpha-beta memory t cell
Macrophage
Mast cell
Epithelial cell
Monocyte
Cd8-positive, alpha-beta memory t cell
Fibroblast
Endothelial cell
Neuronal receptor cell
B cell
Plasma cell
Mature nk t cell
Tissue
Right colon
Developmental stage
16-year-old stage
14-year-old stage
15-year-old stage
8-year-old stage
10-year-old stage
17-year-old stage
13-year-old stage
9-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE305528
CELLxGENE
35,954 cells
•
Dong et al., 2024
Transcriptome Analysis of Archived Tumor Tissues by Visium, GeoMx DSP, and Chromium Methods Reveals Inter- and Intra-Patient Heterogeneity
Explore
h5ad
Homo sapiens
Homo sapiens
Capillary endothelial cell
+18
Capillary endothelial cell
Lung parenchyma
Lung parenchyma
Adult stage
Adult stage
Lung adenocarcinoma
+1
Lung adenocarcinoma
10x gene expression flex
10x gene expression flex
Cell
Cell
Organism
Homo sapiens
Cell type
Capillary endothelial cell
Activated cd8-positive, alpha-beta t cell
Classical monocyte
Cd4-positive, alpha-beta memory t cell
Natural t-regulatory cell
Cytotoxic t cell
Macrophage
Mast cell
Epithelial cell of lung
Dendritic cell, human
Granulocyte
Conventional dendritic cell
Malignant cell
Pericyte
Plasma cell
Plasmacytoid dendritic cell
Fibroblast of lung
Smooth muscle cell
Natural killer cell
Tissue
Lung parenchyma
Developmental stage
Adult stage
Disease
Lung adenocarcinoma
Squamous cell lung carcinoma
Sex
Technology
10x gene expression flex
Suspension type
Cell
Related Links
ArrayExpress BioStudies:E-MTAB-14560
ArrayExpress BioStudies:E-MTAB-14566
Github:bdsc-tds/mosaic_pilot_study
CELLxGENE
35,896 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
+13
Kidney loop of henle thick ascending limb epithelial cell
Kidney
Kidney
13-week-old stage
13-week-old stage
Normal
Normal
Male
Male
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Kidney loop of henle thick ascending limb epithelial cell
Kidney granular cell
Leukocyte
Macrophage
Kidney distal convoluted tubule epithelial cell
Kidney interstitial fibroblast
Kidney collecting duct principal cell
Macula densa epithelial cell
Blood vessel smooth muscle cell
Kidney collecting duct intercalated cell
Podocyte
Endothelial 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
Github:marshalljamie/Kidney-Slide-seq
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
Github:MacoskoLab/slideseq-tools
grekalab.org
GEO series:GSE190094
CELLxGENE
35,839 cells
•
Liu et al., 2022
Spatial maps of T cell receptors and transcriptomes reveal distinct immune niches and interactions in the adaptive immune response
Explore
h5ad
Homo sapiens
Homo sapiens
Cd4-positive helper t cell
+7
Cd4-positive helper t cell
Lung
Lung
61-year-old stage
61-year-old stage
Renal cell carcinoma
Renal cell carcinoma
Male
Male
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
Cd4-positive helper t cell
Malignant cell
B cell
Cd8-positive, alpha-beta t cell
Plasma cell
Regulatory t cell
Exhausted t cell
Myeloid cell
Tissue
Lung
Developmental stage
61-year-old stage
Disease
Renal cell carcinoma
Sex
Male
Technology
Slide-seqv2
Suspension type
Related Links
BroadInstitute Single-Cell Portal:SCP1348/slide-tcr-seq-data
Github:soph-liu/Slide-TCR-seq
CELLxGENE
35,718 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
Macrophage
+11
Macrophage
Spleen
Spleen
3-month-old stage
+3
3-month-old stage
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Mus musculus
Cell type
Macrophage
Megakaryocyte-erythroid progenitor cell
Macrophage dendritic cell progenitor
Granulocyte
Erythroblast
B cell
Immature nk t cell
Plasma cell
Mature nk t cell
T cell
Proerythroblast
Natural killer cell
Tissue
Spleen
Developmental stage
3-month-old stage
20-month-old stage and over
18-month-old stage
4-week-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
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
CELLxGENE
35,699 cells
•
Wang et al., 2023
Dysregulated lung stroma drives emphysema exacerbation by potentiating resident lymphocytes to suppress an epithelial stem cell reservoir
Explore
h5ad
Homo sapiens
Homo sapiens
Macrophage
+8
Macrophage
Alveolus of lung
Alveolus of lung
60-year-old stage
+4
60-year-old stage
Normal
+1
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Macrophage
Alveolar macrophage
Mast cell
Monocyte
B cell
Dendritic cell
Plasma cell
T cell
Natural killer cell
Tissue
Alveolus of lung
Developmental stage
60-year-old stage
65-year-old stage
63-year-old stage
61-year-old stage
73-year-old stage
Disease
Normal
Pulmonary emphysema
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE196638
HumanCellAtlas:f7b46477-0f2a-4bff-a9b7-719e000499a3
CELLxGENE
35,637 cells
Explore
h5ad
Homo sapiens
Homo sapiens
Astrocyte
+8
Astrocyte
Cerebellum
Cerebellum
Pediatric stage
Pediatric stage
Normal
+1
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Astrocyte
Oligodendrocyte precursor cell
Oligodendrocyte
Macrophage
Bergmann glial cell
Interneuron
Endothelial cell
T cell
Neuron
Tissue
Cerebellum
Developmental stage
Pediatric stage
Disease
Normal
Pilocytic astrocytoma
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
HumanCellAtlas:575c0ad9-c78e-469b-9fdf-9a68dd881137
Single Cell Portal
35,551 cells
Explore
Mus musculus
Mus musculus
Pituitary gland cell
Pituitary gland cell
Normal
Normal
10x 3' v3
10x 3' v3
Organism
Mus musculus
Cell type
Pituitary gland cell
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
1
2
…
69
70
71
72
73
…
387
388
Close