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Technology
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Cell
896
Nucleus
659
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Asap
43
Bgee
40
Cellxgene
2,080
Single cell portal
183
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Most cells
Fewest cells
2346
datasets
CELLxGENE
8,643 cells
•
Kanemaru et al., 2023
Spatially resolved multiomics of human cardiac niches
Explore
h5ad
Homo sapiens
Homo sapiens
Neutrophil
+21
Neutrophil
Interventricular septum
Interventricular septum
Sixth decade stage
+2
Sixth decade stage
Normal
Normal
Female
+1
Female
Visium spatial gene expression v1
Visium spatial gene expression v1
Organism
Homo sapiens
Cell type
Neutrophil
Endocardial cell
Dendritic cell, human
Endothelial cell of lymphatic vessel
Mature nk t cell
Mast cell
Cd8-positive, alpha-beta t cell
Endothelial cell of artery
Smooth muscle cell
Smooth muscle cell of the pulmonary artery
Macrophage
Innate lymphoid cell
Glial cell
Vein endothelial cell
Cd14-positive monocyte
Cd14-low, cd16-positive monocyte
Pericyte
Naive thymus-derived cd4-positive, alpha-beta t cell
Mucosal invariant t cell
Monocyte
Regular ventricular cardiac myocyte
Fibroblast of cardiac tissue
Tissue
Interventricular septum
Developmental stage
Sixth decade stage
Fifth decade stage
Seventh decade stage
Disease
Normal
Sex
Female
Male
Technology
Visium spatial gene expression v1
Suspension type
Related Links
heartcellatlas.org
ArrayExpress BioStudies:E-MTAB-12916
ArrayExpress BioStudies:E-MTAB-12919
HumanCellAtlas:925f9a4c-cac0-444a-ad2c-612656ab3a85
ArrayExpress BioStudies:E-MTAB-12975
CELLxGENE
8,613 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
Endocardial cell
+8
Endocardial cell
Heart
Heart
4-week-old stage
+3
4-week-old stage
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Mus musculus
Cell type
Endocardial cell
Erythrocyte
Mast cell
Leukocyte
Smooth muscle cell
Cardiac neuron
Endothelial cell of coronary artery
Cardiac muscle cell
Fibroblast of cardiac tissue
Tissue
Heart
Developmental stage
4-week-old stage
3-month-old stage
20-month-old stage and over
18-month-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
8,573 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
+26
Midbrain-derived inhibitory neuron
Ventral anterior nucleus of thalamus
Ventral anterior 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
Amygdala excitatory neuron
Committed oligodendrocyte precursor
Lamp5 lhx6 neuron
Eccentric medium spiny neuron
Pvalb chandelier gabaergic interneuron
Medial ganglionic eminence derived interneuron
Ependymal cell
Microglial cell
Thalamic excitatory neuron
Pericyte
Cerebral cortex neuron
Neuron
Monocyte
Intratelencephalic-projecting glutamatergic cortical neuron
Caudal ganglionic eminence derived interneuron
Vascular associated smooth muscle cell
Sst chodl gabaergic interneuron
Astrocyte
Fibroblast
Medium spiny neuron
Tissue
Ventral anterior nucleus of 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
CELLxGENE
8,556 cells
•
Barnes et al., 2023
Early human lung immune cell development and its role in epithelial cell fate
Explore
h5ad
Homo sapiens
Homo sapiens
Pulmonary alveolar epithelial cell
+3
Pulmonary alveolar epithelial cell
Lung
Lung
Normal
Normal
10x 5' transcription profiling
10x 5' transcription profiling
Cell
Cell
Organism
Homo sapiens
Cell type
Pulmonary alveolar epithelial cell
Pulmonary neuroendocrine cell
Respiratory tract epithelial cell
Pulmonary alveolar type 2 cell
Tissue
Lung
Developmental stage
Disease
Normal
Sex
Technology
10x 5' transcription profiling
Suspension type
Cell
Related Links
fetal-lung-immune.cellgeni.sanger.ac.uk
ArrayExpress BioStudies:E-MTAB-11528
Github:Peng-He-Lab/lung-immune-cell-atlas
CELLxGENE
8,461 cells
Explore
h5ad
Homo sapiens
Homo sapiens
Natural killer cell
+15
Natural killer cell
Forebrain meninges
+2
Forebrain meninges
13th week post-fertilization stage
+8
13th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Natural killer cell
Mast cell
Platelet
Mucosa-associated lymphoid tissue macrophage
Choroid plexus macrophage
Microglial cell
Innate lymphoid cell
Meningeal macrophage
Common myeloid progenitor
Megakaryocyte
Metamyelocyte
B cell
Promyelocyte
Perivascular macrophage
Monocyte
Dendritic cell
Tissue
Forebrain meninges
Brain meninx
Meninx
Developmental stage
13th week post-fertilization stage
12th week post-fertilization stage
Carnegie stage 20
9th week post-fertilization stage
Carnegie stage 23
10th week post-fertilization stage
Carnegie stage 21
Carnegie stage 16
Carnegie stage 18
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:linnarsson-lab/human-meninges-development
CELLxGENE
8,444 cells
•
MacParland et al., 2018
Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell of hepatic sinusoid
+12
Endothelial cell of hepatic sinusoid
Liver
Liver
21-year-old stage
+4
21-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Endothelial cell of hepatic sinusoid
Hepatocyte
Endothelial cell of periportal hepatic sinusoid
Erythrocyte
Gamma-delta t cell
Alpha-beta t cell
Inflammatory macrophage
Hepatic stellate cell
Macrophage
Innate lymphoid cell
Cholangiocyte
Plasma cell
B cell
Tissue
Liver
Developmental stage
21-year-old stage
65-year-old stage
26-year-old stage
44-year-old stage
41-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
baderlab.org
GEO series:GSE115469
Single Cell Expression Atlas Experiment:E-HCAD-9
UCSC Cell Browser:human-liver
HumanCellAtlas:4d6f6c96-2a83-43d8-8fe1-0f53bffd4674
Bgee
8,444 cells
•
MacParland et al., 2018
Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations
Explore
scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens (tsv.gz)
scRNA-Seq droplet-based H5AD data per cell in Homo sapiens (h5ad)
Homo sapiens
Homo sapiens
Hepatocyte
+13
Hepatocyte
Caudate lobe of liver
Caudate lobe of liver
Life cycle
Life cycle
Normal
Normal
10x genomics v2
10x genomics v2
Organism
Homo sapiens
Cell type
Hepatocyte
Endothelial cell of periportal hepatic sinusoid
Gamma-delta t cell
Alpha-beta t cell
Endothelial cell of hepatic portal vein
Inflammatory macrophage
Erythroid lineage cell
Leukocyte
Hepatic stellate cell
Macrophage
Endothelial cell of pericentral hepatic sinusoid
Mature b cell
Cholangiocyte
Plasma cell
Tissue
Caudate lobe of liver
Developmental stage
Life cycle
Disease
Normal
Sex
Technology
10x genomics v2
Suspension type
Related Links
SRA Project:SRP149989
CELLxGENE
8,425 cells
•
Sampath Kumar et al., 2023
Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis
Explore
h5ad
Mus musculus
Mus musculus
Cardiac valve cell
+14
Cardiac valve cell
Embryo
Embryo
Theiler stage 14
Theiler stage 14
Normal
Normal
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Cardiac valve cell
Spinal cord interneuron
Premigratory neural crest cell
Paraxial cell
Notochordal cell
Neuroplacodal cell
Neurectodermal cell
Hemangioblast
Mesodermal cell
Gut endothelial cell
Primitive red blood cell
Splanchnic mesodermal cell
Surface ectodermal cell
Midbrain dopaminergic neuron
Endodermal cell
Tissue
Embryo
Developmental stage
Theiler stage 14
Disease
Normal
Sex
Technology
Slide-seqv2
Suspension type
Related Links
Chen Lab
GEO series:GSE197353
figshare.com
FigShare Dataset:E9_0_Embryo_h5ad/21695879/1
FigShare Dataset:E8_5_Embryo2_h5ad/21695849/1
Bgee
8,413 cells
•
Murat et al., 2022
The molecular evolution of spermatogenesis across mammals
Explore
scRNA-Seq droplet-based processed expression values per cell population in Gallus gallus (tsv.gz)
scRNA-Seq droplet-based H5AD data per cell in Gallus gallus (h5ad)
Gallus gallus
Gallus gallus
Early spermatid
+5
Early spermatid
Testis
Testis
Post-juvenile adult stage
Post-juvenile adult stage
Normal
Normal
Male
Male
10x genomics v3
10x genomics v3
Organism
Gallus gallus
Cell type
Early spermatid
Sertoli cell
Late spermatid
Obsolete somatic cell
Spermatocyte
Spermatogonium
Tissue
Testis
Developmental stage
Post-juvenile adult stage
Disease
Normal
Sex
Male
Technology
10x genomics v3
Suspension type
Related Links
ebi.ac.uk
CELLxGENE
8,365 cells
•
de Morree et al., 2025
A molecular cell atlas of mouse lemur, an emerging model primate
Explore
h5ad
Microcebus murinus
Microcebus murinus
Endothelial cell of hepatic sinusoid
+21
Endothelial cell of hepatic sinusoid
Liver
Liver
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
Endothelial cell of hepatic sinusoid
Neutrophil
Hepatocyte
Natural killer cell
Endothelial cell
Mature nk t cell
Hematopoietic precursor cell
Cd8-positive, alpha-beta t cell
Erythroid lineage cell
Plasmacytoid dendritic cell
Lymphocyte
Macrophage
Plasma cell
Cd4-positive, alpha-beta t cell
Mesothelial cell
B cell
Monocyte
Basophil
Conventional dendritic cell
Fibroblast
Dendritic cell
Intrahepatic cholangiocyte
Tissue
Liver
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
8,362 cells
•
Leng et al., 2021
Molecular characterization of selectively vulnerable neurons in Alzheimer’s disease
Explore
h5ad
Homo sapiens
Homo sapiens
Glutamatergic neuron
Glutamatergic neuron
Entorhinal cortex
Entorhinal cortex
87-year-old stage
+7
87-year-old stage
Normal
+1
Normal
Male
Male
10x 3' v2
10x 3' v2
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Glutamatergic neuron
Tissue
Entorhinal cortex
Developmental stage
87-year-old stage
71-year-old stage
82-year-old stage
50-year-old stage
72-year-old stage
80 year-old and over stage
77-year-old stage
60-year-old stage
Disease
Normal
Alzheimer disease
Sex
Male
Technology
10x 3' v2
Suspension type
Nucleus
Related Links
GEO series:GSE147528
kampmannlab.ucsf.edu
synapse.org:#!Synapse:syn21788402/wiki/601825
HumanCellAtlas:7dcffc32-7c82-4396-9a4f-88b5579bfe8a
CELLxGENE
8,345 cells
•
Stewart et al., 2019
Spatiotemporal immune zonation of the human kidney
Explore
h5ad
Homo sapiens
Homo sapiens
Neuron
+3
Neuron
Kidney
Kidney
13th week post-fertilization stage
+5
13th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Neuron
Mesenchymal stem cell
Myofibroblast cell
Fibroblast
Tissue
Kidney
Developmental stage
13th week post-fertilization stage
12th week post-fertilization stage
16th week post-fertilization stage
9th week post-fertilization stage
10th week post-fertilization stage
Embryonic stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
kidneycellatlas.org
HumanCellAtlas:abe1a013-af7a-45ed-8c26-f3793c24a1f4
UCSC Cell Browser:kidney-atlas
Single Cell Expression Atlas Experiment:E-HCAD-10
UCSC Genome Browser:hgTrackUi?db=hg38&g=kidneyStewart&position=default
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