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Disease
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Technology
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Cell
896
Nucleus
659
Data Source
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Asap
43
Bgee
40
Cellxgene
2,080
Single cell portal
183
Sort
Most cells
Fewest cells
2346
datasets
CELLxGENE
13,417 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
Macrophage
+1
Macrophage
Brain
Brain
3-month-old stage
+2
3-month-old stage
Normal
Normal
Female
+1
Female
Smart-seq2
Smart-seq2
Cell
Cell
Organism
Mus musculus
Cell type
Macrophage
Microglial cell
Tissue
Brain
Developmental stage
3-month-old stage
20-month-old stage and over
18-month-old stage
Disease
Normal
Sex
Female
Male
Technology
Smart-seq2
Suspension type
Cell
Related Links
GEO series:GSE132042
FigShare Dataset:Processed_files_to_use_with_scanpy_/8273102/2
protocols.io:smartseq2-for-htp-generation-of-facs-sorted-single-2uwgexe
Github:czbiohub/tabula-muris-senis
CZ BioHub Portal:tabula-muris-senis
CELLxGENE
13,382 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Midbrain-derived inhibitory neuron
+22
Midbrain-derived inhibitory neuron
Nucleus of dorsal thalamus
Nucleus of dorsal thalamus
50-year-old stage
50-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Midbrain-derived inhibitory neuron
T cell
Central nervous system macrophage
Natural killer cell
Oligodendrocyte precursor cell
Endothelial cell
Oligodendrocyte
Committed oligodendrocyte precursor
Lamp5 lhx6 neuron
Medial ganglionic eminence derived interneuron
Ependymal cell
Microglial cell
Thalamic excitatory neuron
Choroid plexus epithelial cell
B cell
Pericyte
Neuron
Monocyte
Intratelencephalic-projecting glutamatergic cortical neuron
Caudal ganglionic eminence derived interneuron
Vascular associated smooth muscle cell
Astrocyte
Fibroblast
Tissue
Nucleus of dorsal thalamus
Developmental stage
50-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
NeMo archive:biccn/grant/u01_lein/linnarsson/transcriptome/sncell/10x_v3/human/raw
Github:linnarsson-lab/adult-human-brain
Github:linnarsson-lab/auto-annotation-ah
Single Cell Portal
13,363 cells
Explore
Mus musculus
Mus musculus
Pituitary gland cell
Pituitary gland cell
Pituitary hormone deficiency, combined, 2
+1
Pituitary hormone deficiency, combined, 2
10x 3' v3
10x 3' v3
Organism
Mus musculus
Cell type
Pituitary gland cell
Tissue
Developmental stage
Disease
Pituitary hormone deficiency, combined, 2
Normal
Sex
Technology
10x 3' v3
Suspension type
CELLxGENE
13,318 cells
•
de Morree et al., 2025
A molecular cell atlas of mouse lemur, an emerging model primate
Explore
h5ad
Microcebus murinus
Microcebus murinus
T cell
+32
T cell
Brown adipose tissue
+4
Brown adipose tissue
Post-juvenile adult stage
Post-juvenile adult stage
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Microcebus murinus
Cell type
T cell
Neutrophil
Granulosa cell
Natural killer cell
Endothelial cell of lymphatic vessel
Non-myelinating schwann cell
Reticular cell
Endothelial cell
Mature nk t cell
Cd8-positive, alpha-beta t cell
Pancreatic acinar cell
Tendon cell
Erythroid lineage cell
Endothelial cell of artery
Capillary endothelial cell
Smooth muscle cell
Epithelial cell
Adipocyte
Macrophage
Urothelial cell
Plasma cell
Cd4-positive, alpha-beta t cell
Vein endothelial cell
Mesothelial cell
B cell
Pericyte
Monocyte
Vascular associated smooth muscle cell
Myofibroblast cell
Basophil
Conventional dendritic cell
Fibroblast
Dendritic cell
Tissue
Brown adipose tissue
Gonadal fat pad
Mesenteric fat pad
Subcutaneous adipose tissue
Adipose tissue
Developmental stage
Post-juvenile adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
tabula-microcebus.sf.czbiohub.org
app.globus.org
UCSC Cell Browser:tabula-microcebus
CELLxGENE
13,173 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Midbrain-derived inhibitory neuron
+21
Midbrain-derived inhibitory neuron
Median tuberal portion
Median tuberal portion
50-year-old stage
50-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Midbrain-derived inhibitory neuron
T cell
Central nervous system macrophage
Natural killer cell
Oligodendrocyte precursor cell
Endothelial cell
Oligodendrocyte
Amygdala excitatory neuron
Committed oligodendrocyte precursor
Lamp5 lhx6 neuron
Pvalb chandelier gabaergic interneuron
Medial ganglionic eminence derived interneuron
Ependymal cell
Microglial cell
B cell
Pericyte
Neuron
Monocyte
Caudal ganglionic eminence derived interneuron
Astrocyte
Fibroblast
Mammillary body neuron
Tissue
Median tuberal portion
Developmental stage
50-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
NeMo archive:biccn/grant/u01_lein/linnarsson/transcriptome/sncell/10x_v3/human/raw
Github:linnarsson-lab/adult-human-brain
Github:linnarsson-lab/auto-annotation-ah
CELLxGENE
13,167 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
+8
T cell
Liver
Liver
55-year-old stage
55-year-old stage
Breast cancer
Breast cancer
Female
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
T cell
Hepatocyte
Endothelial cell
Mature nk t cell
Macrophage
Malignant cell
B cell
Monocyte
Fibroblast
Tissue
Liver
Developmental stage
55-year-old stage
Disease
Breast cancer
Sex
Female
Technology
10x 3' v2
Suspension type
Cell
Related Links
humantumoratlas.org
dbGaP Study:phs002371
CELLxGENE
13,165 cells
•
Triana et al., 2021
Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states
Explore
h5ad
Homo sapiens
Homo sapiens
Natural killer cell
+34
Natural killer cell
Bone marrow
Bone marrow
26-year-old stage
26-year-old stage
Normal
Normal
Male
Male
Bd rhapsody whole transcriptome analysis
Bd rhapsody whole transcriptome analysis
Cell
Cell
Organism
Homo sapiens
Cell type
Natural killer cell
Erythroid progenitor cell
Small pre-b-ii cell
Gamma-delta t cell
Pro-b cell
Erythroid lineage cell
Classical monocyte
Pre-natural killer cell
Plasmacytoid dendritic cell
Precursor b cell
Lymphoid lineage restricted progenitor cell
Basophil mast progenitor cell
Megakaryocyte progenitor cell
Common dendritic progenitor
Cd8-positive, alpha-beta memory t cell
Naive thymus-derived cd8-positive, alpha-beta t cell
Unswitched memory b cell
Cd16-positive, cd56-dim natural killer cell, human
Myelocyte
Plasma cell
Late promyelocyte
Hematopoietic multipotent progenitor cell
Cd4-positive, alpha-beta memory t cell
Naive thymus-derived cd4-positive, alpha-beta t cell
Early promyelocyte
Immature b cell
Megakaryocyte-erythroid progenitor cell
Fraction a pre-pro b cell
Central memory cd8-positive, alpha-beta t cell
Naive b cell
Conventional dendritic cell
Class switched memory b cell
Cd16-negative, cd56-bright natural killer cell, human
Effector memory cd8-positive, alpha-beta t cell
Non-classical monocyte
Tissue
Bone marrow
Developmental stage
26-year-old stage
Disease
Normal
Sex
Male
Technology
Bd rhapsody whole transcriptome analysis
Suspension type
Cell
Related Links
EGA Study:EGAS00001005593
EMBL GitLab:triana/nrn
figshare.com
figshare.com
abseqapp.shiny.embl.de
CELLxGENE
13,161 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
Umbrella cell of urothelium
+7
Umbrella cell of urothelium
Ureter
Ureter
69-year-old stage
69-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Umbrella cell of urothelium
Endothelial cell
Leukocyte
Smooth muscle cell
Basal cell of urothelium
Intermediate cell of urothelium
Monocyte
Fibroblast
Tissue
Ureter
Developmental stage
69-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE184111
GEO series:GSE184112
Zenodo record:6762182
Github:2019surbhi/tinglab_ureter_analysis
UCSC Cell Browser:adult-ureter
CELLxGENE
13,147 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
+15
Podocyte
Cortex of kidney
Cortex of kidney
75-year-old stage
75-year-old stage
Normal
Normal
Male
Male
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
Podocyte
Parietal epithelial cell
Endothelial cell
Kidney loop of henle thin descending limb epithelial cell
Kidney interstitial fibroblast
Blood vessel smooth muscle cell
Kidney collecting duct intercalated cell
Leukocyte
Kidney distal convoluted tubule epithelial cell
Kidney collecting duct principal cell
Kidney connecting tubule epithelial cell
Kidney loop of henle thick ascending limb epithelial cell
Kidney loop of henle epithelial cell
Mesangial cell
Pericyte
Kidney proximal convoluted tubule epithelial cell
Tissue
Cortex of kidney
Developmental stage
75-year-old stage
Disease
Normal
Sex
Male
Technology
Slide-seqv2
Suspension type
Related Links
Github:marshalljamie/Kidney-Slide-seq
Github:MacoskoLab/slideseq-tools
grekalab.org
GEO series:GSE190094
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
ASAP
13,143 cells
•
Li et al., 2022
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly
Explore
h5ad
Drosophila melanogaster
Drosophila melanogaster
Hemocyte
+1
Hemocyte
Male reproductive gland
Male reproductive gland
Day 2 of adulthood
Day 2 of adulthood
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Organism
Drosophila melanogaster
Cell type
Hemocyte
Muscle cell
Tissue
Male reproductive gland
Developmental stage
Day 2 of adulthood
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Related Links
ArrayExpress BioStudies:E-MTAB-10519
CELLxGENE
12,964 cells
•
Santo et al., 2025
Exploring the utility of snRNA-seq in profiling human bladder tissue: A comprehensive comparison with scRNA-seq
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell of lymphatic vessel
+7
Endothelial cell of lymphatic vessel
Urinary bladder
Urinary bladder
21-year-old stage
21-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Cell
+1
Cell
Organism
Homo sapiens
Cell type
Endothelial cell of lymphatic vessel
Endothelial cell
Endothelial cell of artery
Schwann cell
Smooth muscle cell
Vein endothelial cell
Vascular associated smooth muscle cell
Fibroblast
Tissue
Urinary bladder
Developmental stage
21-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Cell
Nucleus
Related Links
GEO series:GSE267964
Github:basanto/Human_Bladder_scRNA-seq_vs_snRNA-seq
CELLxGENE
12,944 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Midbrain-derived inhibitory neuron
+20
Midbrain-derived inhibitory neuron
Centromedian nucleus of thalamus
Centromedian nucleus of thalamus
50-year-old stage
50-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Midbrain-derived inhibitory neuron
T cell
Central nervous system macrophage
Natural killer cell
Oligodendrocyte precursor cell
Endothelial cell
Oligodendrocyte
Committed oligodendrocyte precursor
Lamp5 lhx6 neuron
Pvalb chandelier gabaergic interneuron
Medial ganglionic eminence derived interneuron
Microglial cell
Thalamic excitatory neuron
B cell
Pericyte
Neuron
Monocyte
Caudal ganglionic eminence derived interneuron
Vascular associated smooth muscle cell
Astrocyte
Fibroblast
Tissue
Centromedian nucleus of thalamus
Developmental stage
50-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
Github:linnarsson-lab/adult-human-brain
Github:linnarsson-lab/auto-annotation-ah
NeMo archive:biccn/grant/u01_lein/linnarsson/transcriptome/sncell/10x_v3/human/raw
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