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Disease
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Sex
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Technology
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Cell
934
Nucleus
679
Data Source
0
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ASAP
79
Bgee
40
CELLxGENE
2,213
Single Cell Portal
183
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Most cells
Fewest cells
2515
datasets
CELLxGENE
12,488 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
64-year-old stage
64-year-old stage
Normal
Normal
Female
Female
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
64-year-old stage
Disease
Normal
Sex
Female
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
12,461 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+25
T cell
Hippocampal field
Hippocampal field
29-year-old stage
29-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
T cell
Central nervous system macrophage
Natural killer cell
Oligodendrocyte precursor cell
Endothelial cell
Oligodendrocyte
Amygdala excitatory neuron
Committed oligodendrocyte precursor
Dentate gyrus granule cell
Hippocampal ca1-3 neuron
Lamp5 lhx6 neuron
Pvalb chandelier gabaergic interneuron
Medial ganglionic eminence derived interneuron
Ependymal cell
Microglial cell
B cell
Pericyte
Cerebral cortex neuron
Near-projecting glutamatergic cortical neuron
Neuron
Intratelencephalic-projecting glutamatergic cortical neuron
Caudal ganglionic eminence derived interneuron
Vascular associated smooth muscle cell
Sst chodl gabaergic interneuron
Astrocyte
Hippocampal ca4 neuron
Tissue
Hippocampal field
Developmental stage
29-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
data.nemoarchive.org
github (analysis and figures)
github (auto-annotations)
CELLxGENE
12,444 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
56-year-old stage
56-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
56-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
CELLxGENE
12,376 cells
•
Zhang et al., 2023
A human embryonic limb cell atlas resolved in space and time
Explore
h5ad
Homo sapiens
Homo sapiens
Muscle cell
+2
Muscle cell
Hindlimb
+1
Hindlimb
Carnegie stage 19
+7
Carnegie stage 19
Normal
Normal
Female
+1
Female
10x 5' v1
+1
10x 5' v1
Cell
Cell
Organism
Homo sapiens
Cell type
Muscle cell
Skeletal muscle myoblast
Myoblast
Tissue
Hindlimb
Forelimb
Developmental stage
Carnegie stage 19
9th week post-fertilization stage
Carnegie stage 23
10th week post-fertilization stage
Carnegie stage 17
Carnegie stage 16
Carnegie stage 15
Carnegie stage 18
Disease
Normal
Sex
Female
Male
Technology
10x 5' v1
10x 3' v2
Suspension type
Cell
Related Links
developmental.cellatlas.io
mouse scRNA-seq
human Visium
human scRNA-seq
github.com
Bgee
12,352 cells
•
Murat et al., 2022
The molecular evolution of spermatogenesis across mammals
Explore
scRNA-Seq droplet-based processed expression values per cell population in Pan troglodytes (tsv.gz)
scRNA-Seq droplet-based H5AD data per cell in Pan troglodytes (h5ad)
Pan troglodytes
Pan troglodytes
Cell
+7
Cell
Testis
Testis
Late adult stage
Late adult stage
Normal
Normal
Male
Male
10x genomics v2
10x genomics v2
Organism
Pan troglodytes
Cell type
Cell
Early spermatid
Sertoli cell
Late spermatid
Male germ line stem cell
Obsolete somatic cell
Spermatocyte
Spermatogonium
Tissue
Testis
Developmental stage
Late adult stage
Disease
Normal
Sex
Male
Technology
10x genomics v2
Suspension type
Related Links
ebi.ac.uk
CELLxGENE
12,351 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
+11
Podocyte
Kidney
Kidney
13-week-old stage
13-week-old stage
Diabetic kidney disease
Diabetic kidney disease
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 collecting duct principal cell
Kidney loop of henle thick ascending limb epithelial cell
Mesangial cell
Kidney proximal convoluted tubule epithelial cell
Tissue
Kidney
Developmental stage
13-week-old stage
Disease
Diabetic kidney disease
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
12,330 cells
•
Escoubas et al., 2024
Type-I-interferon-responsive microglia shape cortical development and behavior
Explore
h5ad
Mus musculus
Mus musculus
Microglial cell
Microglial cell
Barrel cortex
Barrel cortex
5-day-old stage
+1
5-day-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Microglial cell
Tissue
Barrel cortex
Developmental stage
5-day-old stage
7-day-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
annamolofskylab.org
GSE173173
lcdorman.shinyapps.io
CELLxGENE
12,295 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
T cell
+6
T cell
Mammary gland
Mammary gland
3-month-old stage
+2
3-month-old stage
Normal
Normal
Female
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Mus musculus
Cell type
T cell
Stromal cell
Endothelial cell
Basal cell
Luminal epithelial cell of mammary gland
Macrophage
B cell
Tissue
Mammary gland
Developmental stage
3-month-old stage
20-month-old stage and over
18-month-old stage
Disease
Normal
Sex
Female
Technology
10x 3' v2
Suspension type
Cell
Related Links
GSE132042
Processed files
Tabula Muris Senis
SmartSeq2 for HTP Generation of FACS Sorted Single Cell Libraries V.1
github.com
CELLxGENE
12,258 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
Endothelial cell of hepatic sinusoid
+10
Endothelial cell of hepatic sinusoid
Liver
Liver
31-year-old stage
31-year-old stage
Breast cancer
Breast cancer
Female
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Endothelial cell of hepatic sinusoid
T cell
Blood vessel endothelial cell
Hepatocyte
Mature nk t cell
Blood vessel smooth muscle cell
Hepatic stellate cell
Macrophage
Malignant cell
Neuron
Fibroblast
Tissue
Liver
Developmental stage
31-year-old stage
Disease
Breast cancer
Sex
Female
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
humantumoratlas.org
phs002371
CELLxGENE
12,205 cells
•
Lazarescu et al., 2025
Human subcutaneous and visceral adipocyte atlases uncover classical and nonclassical adipocytes and depot-specific patterns
Explore
h5ad
Homo sapiens
Homo sapiens
Subcutaneous adipocyte
Subcutaneous adipocyte
Subcutaneous adipose tissue
Subcutaneous adipose tissue
34-year-old stage
+3
34-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Subcutaneous adipocyte
Tissue
Subcutaneous adipose tissue
Developmental stage
34-year-old stage
24-year-old stage
33-year-old stage
41-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
Zenodo code
GSE281356
HCA
CELLxGENE
12,162 cells
•
Fink et al., 2022
Single-cell and spatial mapping Identify cell types and signaling Networks in the human ureter
Explore
h5ad
Homo sapiens
Homo sapiens
Central memory cd4-positive, alpha-beta t cell
+12
Central memory cd4-positive, alpha-beta t cell
Ureter
Ureter
69-year-old stage
+8
69-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Central memory cd4-positive, alpha-beta t cell
Effector cd8-positive, alpha-beta t cell
Mature nk t cell
Mast cell
Classical monocyte
Cd8-positive, alpha-beta memory t cell
Macrophage
Regulatory t cell
B cell
Mucosal invariant t cell
Double negative thymocyte
Dendritic cell
Non-classical monocyte
Tissue
Ureter
Developmental stage
69-year-old stage
75-year-old stage
65-year-old stage
85-year-old stage
68-year-old stage
82-year-old stage
81-year-old stage
74-year-old stage
79-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
GSE184111
GSE184112
cells.ucsc.edu
zenodo.org
github.com
CELLxGENE
12,132 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
+11
Podocyte
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
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 collecting duct principal cell
Kidney loop of henle thick ascending limb epithelial cell
Mesangial cell
Kidney proximal 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
ncbi.nlm.nih.gov
Kidney Slide-seq Github
protocols.io
Macosko Lab Slide-seq Github
grekalab.org
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