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Disease
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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
Sort
Most cells
Fewest cells
2346
datasets
CELLxGENE
17,622 cells
•
Fawkner-Corbett et al., 2021
Spatiotemporal analysis of human intestinal development at single-cell resolution
Explore
h5ad
Homo sapiens
Homo sapiens
Transit amplifying cell of small intestine
+9
Transit amplifying cell of small intestine
Hindgut
+2
Hindgut
19th week post-fertilization stage
+11
19th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Transit amplifying cell of small intestine
Intestine goblet cell
Intestinal crypt stem cell of large intestine
Secretory cell
Gut absorptive cell
Enteroendocrine cell
Transit amplifying cell of colon
Enterocyte
Progenitor cell
Intestinal crypt stem cell of small intestine
Tissue
Hindgut
Ileum
Colon
Developmental stage
19th week post-fertilization stage
21st week post-fertilization stage
23rd week post-fertilization stage
13th week post-fertilization stage
14th week post-fertilization stage
20th week post-fertilization stage
17th week post-fertilization stage
16th week post-fertilization stage
10th week post-fertilization stage
18th week post-fertilization stage
Carnegie stage 22
11th week post-fertilization stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE158328
simmonslab.shinyapps.io
Mendeley Data Dataset:gncg57p5x9/2
dropbox.com
GEO series:GSE158702
HumanCellAtlas:fa3f460f-4fb9-4ced-b548-8ba6a8ecae3f
CELLxGENE
17,613 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
Hemangioblast
Mesodermal cell
Gut endothelial cell
Primitive red blood cell
Splanchnic mesodermal cell
Surface ectodermal cell
Midbrain dopaminergic neuron
Endodermal cell
Anterior visceral endoderm 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
CELLxGENE
17,612 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
Epithelial cell
+3
Epithelial cell
Kidney
Kidney
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
Epithelial cell
Myeloid cell
Malignant cell
Fibroblast
Tissue
Kidney
Developmental stage
61-year-old stage
Disease
Renal cell carcinoma
Sex
Male
Technology
Slide-seqv2
Suspension type
Related Links
Github:soph-liu/Slide-TCR-seq
BroadInstitute Single-Cell Portal:SCP1348/slide-tcr-seq-data
CELLxGENE
17,598 cells
•
Duran et al., 2025
A statistical framework for inferring genetic requirements from embryo-scale single-cell sequencing experiments
Explore
h5ad
Danio rerio
Danio rerio
Stromal cell
+3
Stromal cell
Heart primordium
+4
Heart primordium
Pharyngula:prim-15
+9
Pharyngula:prim-15
Normal
Normal
Sci-rna-seq3
Sci-rna-seq3
Nucleus
Nucleus
Organism
Danio rerio
Cell type
Stromal cell
Mesodermal cell
Splanchnic mesodermal cell
Mesothelial cell
Tissue
Heart primordium
Anterior lateral plate mesoderm
Lateral plate mesoderm
Proepicardium
Pronephric mesoderm
Developmental stage
Pharyngula:prim-15
Hatching:long-pec
Larval:protruding-mouth
Pharyngula:prim-25
Segmentation:26+ somites
Segmentation:14-19 somites
Hatching:pec-fin
Segmentation:20-25 somites
Pharyngula:high-pec
Pharyngula:prim-5
Disease
Normal
Sex
Technology
Sci-rna-seq3
Suspension type
Nucleus
Related Links
GEO series:GSE295164
cole-trapnelllab.github.io
DOI:10.1038/s41586-023-06720-2
CELLxGENE
17,586 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
+13
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
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
figshare.com
FigShare Dataset:E8_5_Embryo2_h5ad/21695849/1
FigShare Dataset:E9_0_Embryo_h5ad/21695879/1
GEO series:GSE197353
CELLxGENE
17,535 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+15
T cell
Brodmann (1909) area 35
Brodmann (1909) area 35
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
T cell
Central nervous system macrophage
Natural killer cell
Oligodendrocyte precursor cell
Endothelial cell
Oligodendrocyte
Amygdala excitatory neuron
Committed oligodendrocyte precursor
Microglial cell
B cell
Pericyte
Neuron
Monocyte
Vascular associated smooth muscle cell
Astrocyte
Fibroblast
Tissue
Brodmann (1909) area 35
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
17,528 cells
•
Kedlian et al., 2024
Human skeletal muscle aging atlas
Explore
h5ad
Homo sapiens
Homo sapiens
Skeletal muscle satellite stem cell
Skeletal muscle satellite stem cell
Intercostal muscle
Intercostal muscle
Sixth decade stage
+5
Sixth decade stage
Normal
Normal
Female
+1
Female
10x 3' v3
+1
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Skeletal muscle satellite stem cell
Tissue
Intercostal muscle
Developmental stage
Sixth decade stage
Third decade stage
Seventh decade stage
Fourth decade stage
Eighth decade stage
Young adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
10x 3' v2
Suspension type
Cell
Related Links
muscleageingcellatlas.org
ArrayExpress BioStudies:E-MTAB-13874
Single Cell Portal
17,512 cells
Explore
Mus musculus
Mus musculus
Granulocyte
+9
Granulocyte
Normal
Normal
Slide-seqv2
+2
Slide-seqv2
Organism
Mus musculus
Cell type
Granulocyte
Cell
Endothelial cell
Mast cell
Lymphocyte
Macrophage
B cell
Colon epithelial cell
Monocyte
Fibroblast
Tissue
Developmental stage
Disease
Normal
Sex
Technology
Slide-seqv2
10x 3' v3
10x 3' v2
Suspension type
CELLxGENE
17,451 cells
•
Lukassen et al., 2020
<scp>SARS</scp> ‐CoV‐2 receptor <scp>ACE</scp> 2 and <scp>TMPRSS</scp> 2 are primarily expressed in bronchial transient secretory cells
Explore
h5ad
Homo sapiens
Homo sapiens
Club cell
+7
Club cell
Respiratory airway
Respiratory airway
53-year-old stage
+2
53-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Club cell
Lung secretory cell
Primary cultured cell
Pulmonary ionocyte
Basal cell
Lung multiciliated epithelial cell
Fibroblast of lung
Tracheal goblet cell
Tissue
Respiratory airway
Developmental stage
53-year-old stage
55-year-old stage
67-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
FigShare Dataset:Single-cell_RNA-Seq_of_human_primary_lung_and_bronchial_epithelium_cells/11981034/1
digital.bihealth.org
Mendeley Data Dataset:7r2cwbw44m/1
UCSC Cell Browser:eils-lung
EGA Study:EGAS00001004419
HumanCellAtlas:58028aa8-0ed2-49ca-b60f-15e2ed5989d5
Single Cell Portal
17,375 cells
Explore
Homo sapiens
Homo sapiens
T cell
+6
T cell
Normal
+1
Normal
10x 5' v1
+1
10x 5' v1
Organism
Homo sapiens
Cell type
T cell
Natural killer cell
Platelet
Plasmacytoid dendritic cell
B cell
Monocyte
Conventional dendritic cell
Tissue
Developmental stage
Disease
Normal
Obsolete type 1 interferonopathy
Sex
Technology
10x 5' v1
10x 3' v3
Suspension type
Single Cell Portal
17,366 cells
Explore
Mus musculus
Mus musculus
Pituitary gland cell
Pituitary gland cell
Normal
Normal
10x 3' v2
10x 3' v2
Organism
Mus musculus
Cell type
Pituitary gland cell
Tissue
Developmental stage
Disease
Normal
Sex
Technology
10x 3' v2
Suspension type
Related Links
DOI:10.1210/en.2018-00750
GEO series:GSE120410
CELLxGENE
17,363 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
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 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
6-month-old stage
Disease
Autosomal dominant polycystic kidney disease
Sex
Male
Technology
Slide-seqv2
Suspension type
Related Links
GEO series:GSE190094
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
Github:MacoskoLab/slideseq-tools
grekalab.org
Github:marshalljamie/Kidney-Slide-seq
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