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Disease
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Technology
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Cell
893
Nucleus
659
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Asap
43
Bgee
40
Cellxgene
2,077
Single cell portal
179
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Most cells
Fewest cells
2339
datasets
CELLxGENE
18,471 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
+8
Kidney loop of henle thick ascending limb epithelial cell
Renal medulla
Renal medulla
54-year-old stage
54-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 interstitial fibroblast
Leukocyte
Kidney collecting duct principal cell
Macrophage
Blood vessel smooth muscle cell
Endothelial cell
Kidney collecting duct intercalated cell
Kidney distal convoluted tubule epithelial cell
Tissue
Renal medulla
Developmental stage
54-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
18,402 cells
•
Gabitto et al., 2024
Integrated multimodal cell atlas of Alzheimer’s disease
Explore
h5ad
Homo sapiens
Homo sapiens
Corticothalamic-projecting glutamatergic cortical neuron
Corticothalamic-projecting glutamatergic cortical neuron
Middle temporal gyrus
Middle temporal gyrus
43-year-old stage
+23
43-year-old stage
Dementia
+1
Dementia
Female
+1
Female
10x multiome
+1
10x multiome
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Corticothalamic-projecting glutamatergic cortical neuron
Tissue
Middle temporal gyrus
Developmental stage
43-year-old stage
68-year-old stage
88-year-old stage
86-year-old stage
82-year-old stage
83-year-old stage
60-year-old stage
75-year-old stage
80-year-old stage
77-year-old stage
Adult stage
89-year-old stage
78-year-old stage
72-year-old stage
80 year-old and over stage
81-year-old stage
87-year-old stage
84-year-old stage
65-year-old stage
85-year-old stage
50-year-old stage
29-year-old stage
69-year-old stage
70-year-old stage
Disease
Dementia
Normal
Sex
Female
Male
Technology
10x multiome
10x 3' v3
Suspension type
Nucleus
Related Links
Alzheimer's Disease Research Center
Adult Changes in Thought Study
BRaIN-lab
AD knowledge portal:syn26223298
AWS Open Data:allen-sea-ad-atlas
Allen Brain Map:seattle-alzheimers-disease
CELLxGENE
18,386 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
Pulmonary alveolar type 2 cell
+8
Pulmonary alveolar type 2 cell
Alveolus of lung
Alveolus of lung
60-year-old stage
+4
60-year-old stage
Pulmonary emphysema
+1
Pulmonary emphysema
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Pulmonary alveolar type 2 cell
Epithelial cell of lower respiratory tract
Ciliated cell
Pericyte
Endothelial cell of lymphatic vessel
Smooth muscle cell
Endothelial cell
Pulmonary alveolar type 1 cell
Fibroblast
Tissue
Alveolus of lung
Developmental stage
60-year-old stage
63-year-old stage
61-year-old stage
65-year-old stage
73-year-old stage
Disease
Pulmonary emphysema
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE196638
HumanCellAtlas:f7b46477-0f2a-4bff-a9b7-719e000499a3
CELLxGENE
18,377 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
+8
Kidney loop of henle thick ascending limb epithelial cell
Renal medulla
Renal medulla
64-year-old stage
64-year-old stage
Normal
Normal
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
Kidney loop of henle thick ascending limb epithelial cell
Kidney interstitial fibroblast
Leukocyte
Kidney collecting duct principal cell
Macrophage
Blood vessel smooth muscle cell
Endothelial cell
Kidney collecting duct intercalated cell
Kidney distal convoluted tubule epithelial cell
Tissue
Renal medulla
Developmental stage
64-year-old stage
Disease
Normal
Sex
Female
Technology
Slide-seqv2
Suspension type
Related Links
GEO series:GSE190094
Github:marshalljamie/Kidney-Slide-seq
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
Github:MacoskoLab/slideseq-tools
grekalab.org
CELLxGENE
18,315 cells
•
Lengyel et al., 2022
A molecular atlas of the human postmenopausal fallopian tube and ovary from single-cell RNA and ATAC sequencing
Explore
h5ad
Homo sapiens
Homo sapiens
Leukocyte
+4
Leukocyte
Ovary
Ovary
62-year-old stage
+2
62-year-old stage
Normal
Normal
Female
Female
10x scatac-seq
10x scatac-seq
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Leukocyte
Pericyte
Smooth muscle cell
Stromal cell
Endothelial cell
Tissue
Ovary
Developmental stage
62-year-old stage
58-year-old stage
65-year-old stage
Disease
Normal
Sex
Female
Technology
10x scatac-seq
Suspension type
Nucleus
Related Links
EGA Study:EGAS00001006780
CELLxGENE
18,297 cells
•
Sampath Kumar et al., 2023
Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis
Explore
h5ad
Mus musculus
Mus musculus
Notochordal cell
+14
Notochordal cell
Embryo
Embryo
Theiler stage 14
Theiler stage 14
Normal
Normal
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Notochordal cell
Spinal cord interneuron
Paraxial cell
Neurectodermal cell
Gut endothelial cell
Splanchnic mesodermal cell
Hemangioblast
Cardiac valve cell
Endodermal cell
Primitive red blood cell
Midbrain dopaminergic neuron
Premigratory neural crest cell
Mesodermal cell
Neuroplacodal cell
Surface ectodermal 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:E8_5_Embryo2_h5ad/21695849/1
FigShare Dataset:E9_0_Embryo_h5ad/21695879/1
CELLxGENE
18,162 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
Autosomal dominant polycystic kidney disease
Autosomal dominant polycystic kidney disease
Male
Male
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Kidney loop of henle thick ascending limb epithelial cell
Kidney interstitial fibroblast
Leukocyte
Kidney proximal convoluted tubule epithelial cell
Podocyte
Kidney collecting duct principal cell
Macrophage
Blood vessel smooth muscle cell
Endothelial cell
Kidney collecting duct intercalated cell
Mesangial cell
Kidney distal 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
Github:marshalljamie/Kidney-Slide-seq
Github:MacoskoLab/slideseq-tools
grekalab.org
GEO series:GSE190094
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
CELLxGENE
18,100 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
Photoreceptor cell
Photoreceptor cell
Multicellular anatomical structure
Multicellular anatomical structure
Segmentation:14-19 somites
+9
Segmentation:14-19 somites
Normal
Normal
Sci-rna-seq3
Sci-rna-seq3
Nucleus
Nucleus
Organism
Danio rerio
Cell type
Photoreceptor cell
Tissue
Multicellular anatomical structure
Developmental stage
Segmentation:14-19 somites
Hatching:pec-fin
Larval:protruding-mouth
Pharyngula:prim-5
Pharyngula:high-pec
Hatching:long-pec
Segmentation:20-25 somites
Segmentation:26+ somites
Pharyngula:prim-15
Pharyngula:prim-25
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
18,011 cells
•
Liang et al., 2023
A multi-omics atlas of the human retina at single-cell resolution
Explore
h5ad
Homo sapiens
Homo sapiens
Astrocyte
+3
Astrocyte
Fovea centralis
+2
Fovea centralis
83-year-old stage
+4
83-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Astrocyte
Microglial cell
Retinal pigment epithelial cell
Mueller cell
Tissue
Fovea centralis
Macula lutea proper
Peripheral region of retina
Developmental stage
83-year-old stage
78-year-old stage
84-year-old stage
65-year-old stage
73-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
UCSC Cell Browser:retina-atac
HumanCellAtlas:9c20a245-f2c0-43ae-82c9-2232ec6b594f
GEO series:GSE226108
CELLxGENE
17,962 cells
•
Hochane et al., 2019
Single-cell transcriptomics reveals gene expression dynamics of human fetal kidney development
Explore
h5ad
Homo sapiens
Homo sapiens
Leukocyte
+9
Leukocyte
Kidney
Kidney
14th week post-fertilization stage
+4
14th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Leukocyte
Kidney cell
Podocyte
Glomerular mesangial cell
Epithelial cell of proximal tubule
Kidney interstitial cell
Endothelial cell
Kidney connecting tubule epithelial cell
Kidney epithelial cell
Mesonephric nephron tubule epithelial cell
Tissue
Kidney
Developmental stage
14th week post-fertilization stage
9th week post-fertilization stage
16th week post-fertilization stage
11th week post-fertilization stage
Carnegie stage 19
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
Suspension type
Cell
Related Links
GEO series:GSE114530
semraulab.com
CELLxGENE
17,909 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
+17
Kidney loop of henle thick ascending limb epithelial cell
Renal medulla
Renal medulla
64-year-old stage
64-year-old stage
Normal
Normal
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
Kidney loop of henle thick ascending limb epithelial cell
Kidney interstitial fibroblast
Kidney inner medulla collecting duct epithelial cell
Leukocyte
Kidney proximal convoluted tubule epithelial cell
Podocyte
Parietal epithelial cell
Pericyte
Kidney collecting duct principal cell
Blood vessel smooth muscle cell
Kidney loop of henle thin descending limb epithelial cell
Endothelial cell
Kidney loop of henle epithelial cell
Urothelial cell
Kidney collecting duct intercalated cell
Mesangial cell
Kidney connecting tubule epithelial cell
Kidney distal convoluted tubule epithelial cell
Tissue
Renal medulla
Developmental stage
64-year-old stage
Disease
Normal
Sex
Female
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
17,891 cells
•
Krienen et al., 2023
A marmoset brain cell census reveals regional specialization of cellular identities
Explore
h5ad
Callithrix jacchus
Callithrix jacchus
Glutamatergic neuron
Glutamatergic neuron
Hippocampal formation
Hippocampal formation
Prime adult stage
Prime adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Callithrix jacchus
Cell type
Glutamatergic neuron
Tissue
Hippocampal formation
Developmental stage
Prime adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
NeMo archive:dat-1je0mn3
submit.brainimagelibrary.org
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