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Organism
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Cell Type
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Tissue
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Developmental Stage
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Disease
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Sex
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Technology
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Suspension Type
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Cell
893
Nucleus
659
Data Source
0
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Asap
43
Bgee
40
Cellxgene
2,077
Single cell portal
179
Sort
Most cells
Fewest cells
2339
datasets
CELLxGENE
11,964 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
Sensory hair cell
+2
Sensory hair cell
Macula
+4
Macula
Segmentation:14-19 somites
+9
Segmentation:14-19 somites
Normal
Normal
Sci-rna-seq3
Sci-rna-seq3
Nucleus
Nucleus
Organism
Danio rerio
Cell type
Sensory hair cell
Auditory epithelial supporting cell
Neurecto-epithelial cell
Tissue
Macula
Crista ampullaris
Semicircular canal
Lateral line
Ear vesicle
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
cole-trapnelllab.github.io
DOI:10.1038/s41586-023-06720-2
GEO series:GSE295164
CELLxGENE
11,851 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
Hepatocyte
+6
Hepatocyte
Liver
Liver
29-year-old stage
29-year-old stage
Breast cancer
Breast cancer
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
Hepatocyte
T cell
Monocyte
Malignant cell
Macrophage
Endothelial cell
Fibroblast
Tissue
Liver
Developmental stage
29-year-old stage
Disease
Breast cancer
Sex
Female
Technology
Slide-seqv2
Suspension type
Related Links
humantumoratlas.org
dbGaP Study:phs002371
ASAP
11,788 cells
•
Li et al., 2022
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly
Explore
h5ad
Drosophila melanogaster
Drosophila melanogaster
Enteroendocrine cell
+1
Enteroendocrine cell
Gut
Gut
Day 5 of adulthood
Day 5 of adulthood
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Organism
Drosophila melanogaster
Cell type
Enteroendocrine cell
Muscle cell
Tissue
Gut
Developmental stage
Day 5 of adulthood
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Related Links
ArrayExpress BioStudies:E-MTAB-10519
Single Cell Portal
11,765 cells
Explore
Mus musculus
Mus musculus
Natural killer cell
+5
Natural killer cell
Encephalitis
Encephalitis
10x 3' v3
10x 3' v3
Organism
Mus musculus
Cell type
Natural killer cell
T cell
B cell
Neutrophil
Monocyte
Macrophage
Tissue
Developmental stage
Disease
Encephalitis
Sex
Technology
10x 3' v3
Suspension type
CELLxGENE
11,617 cells
•
Liang et al., 2023
A multi-omics atlas of the human retina at single-cell resolution
Explore
h5ad
Homo sapiens
Homo sapiens
Retinal ganglion cell
Retinal ganglion cell
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
Retinal ganglion 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
11,574 cells
•
Szabo et al., 2021
Longitudinal profiling of respiratory and systemic immune responses reveals myeloid cell-driven lung inflammation in severe COVID-19
Explore
h5ad
Homo sapiens
Homo sapiens
Dendritic cell
+7
Dendritic cell
Blood
Blood
49-year-old stage
49-year-old stage
Covid-19
Covid-19
Male
Male
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Dendritic cell
B cell
Neutrophil
Platelet
Mature nk t cell
Erythrocyte
Plasma cell
Myeloid cell
Tissue
Blood
Developmental stage
49-year-old stage
Disease
Covid-19
Sex
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
Mendeley Data Dataset:fm7v43jrbk/2
Github:simslab/cluster_diffex2018
COVID-19 cell atlas
CELLxGENE
11,510 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
Mus musculus
Mus musculus
Natural killer cell
+5
Natural killer cell
Spleen
Spleen
Normal
Normal
Slide-seqv2
Slide-seqv2
Organism
Mus musculus
Cell type
Natural killer cell
B cell
Memory t cell
Cd8-positive, alpha-beta t cell
Myeloid cell
Cd4-positive helper t cell
Tissue
Spleen
Developmental stage
Disease
Normal
Sex
Technology
Slide-seqv2
Suspension type
Related Links
Github:soph-liu/Slide-TCR-seq
BroadInstitute Single-Cell Portal:SCP1348/slide-tcr-seq-data
CELLxGENE
11,484 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
Hepatocyte
+8
Hepatocyte
Liver
Liver
40-year-old stage
40-year-old stage
Breast cancer
Breast cancer
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
Hepatocyte
T cell
Monocyte
Malignant cell
Mature nk t cell
Macrophage
Endothelial cell
Fibroblast
Plasma cell
Tissue
Liver
Developmental stage
40-year-old stage
Disease
Breast cancer
Sex
Female
Technology
Slide-seqv2
Suspension type
Related Links
humantumoratlas.org
dbGaP Study:phs002371
CELLxGENE
11,456 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
+12
Kidney loop of henle thick ascending limb epithelial cell
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
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 granular cell
Kidney distal 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
Github:marshalljamie/Kidney-Slide-seq
protocols.io:library-generation-using-slide-seqv2-bpgzmjx6
Github:MacoskoLab/slideseq-tools
grekalab.org
GEO series:GSE190094
Single Cell Portal
11,455 cells
Explore
Mus musculus
Mus musculus
Kupffer cell
+2
Kupffer cell
Fibrotic liver disease
+1
Fibrotic liver disease
10x 3' transcription profiling
10x 3' transcription profiling
Organism
Mus musculus
Cell type
Kupffer cell
Monocyte
Macrophage
Tissue
Developmental stage
Disease
Fibrotic liver disease
Normal
Sex
Technology
10x 3' transcription profiling
Suspension type
CELLxGENE
11,430 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
Hepatocyte
+8
Hepatocyte
Liver
Liver
57-year-old stage
57-year-old stage
Breast cancer
Breast cancer
Female
Female
Slide-seqv2
Slide-seqv2
Organism
Homo sapiens
Cell type
Hepatocyte
T cell
B cell
Monocyte
Malignant cell
Mature nk t cell
Macrophage
Endothelial cell
Fibroblast
Tissue
Liver
Developmental stage
57-year-old stage
Disease
Breast cancer
Sex
Female
Technology
Slide-seqv2
Suspension type
Related Links
humantumoratlas.org
dbGaP Study:phs002371
CELLxGENE
11,404 cells
•
Yan et al., 2020
Cell Atlas of The Human Fovea and Peripheral Retina
Explore
h5ad
Homo sapiens
Homo sapiens
Retinal ganglion cell
Retinal ganglion cell
Fovea centralis
+1
Fovea centralis
64-year-old stage
+6
64-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v2
+1
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Retinal ganglion cell
Tissue
Fovea centralis
Peripheral region of retina
Developmental stage
64-year-old stage
60-year-old stage
74-year-old stage
78-year-old stage
65-year-old stage
53-year-old stage
69-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
10x 3' v3
Suspension type
Cell
Related Links
GEO series:GSE148077
HumanCellAtlas:30dc3964-1135-4b56-b393-ce2dcbc6e379
BroadInstitute Single-Cell Portal:SCP839/cell-atlas-of-the-human-fovea-and-peripheral-retina
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