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Tissue
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Disease
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Technology
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Cell
893
Nucleus
659
Data Source
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Asap
43
Bgee
40
Cellxgene
2,077
Single cell portal
179
Sort
Most cells
Fewest cells
2339
datasets
CELLxGENE
9,110 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
Epithelial cell of distal tubule
+5
Epithelial cell of distal tubule
Multicellular anatomical structure
+5
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
Epithelial cell of distal tubule
Kidney proximal convoluted tubule epithelial cell
Podocyte
Multiciliated epithelial cell
Endocrine cell
Mesodermal cell
Tissue
Multicellular anatomical structure
Proximal convoluted tubule
Distal tubule
Pronephros
Corpuscles of stannius
Pronephric glomerulus
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
9,096 cells
•
He et al., 2022
A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates
Explore
h5ad
Homo sapiens
Homo sapiens
Pulmonary alveolar type 2 cell
+10
Pulmonary alveolar type 2 cell
Lung
Lung
9th week post-fertilization stage
+7
9th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x 5' v1
10x 5' v1
Cell
Cell
Organism
Homo sapiens
Cell type
Pulmonary alveolar type 2 cell
Club cell
Glandular secretory epithelial cell
Epithelial cell of lung
Neuroendocrine cell
Lung secretory cell
Basal cell
Respiratory tract epithelial cell
Squamous epithelial cell
Pulmonary alveolar type 1 cell
Pulmonary neuroendocrine cell
Tissue
Lung
Developmental stage
9th week post-fertilization stage
11th week post-fertilization stage
Carnegie stage 16
15th week post-fertilization stage
20th week post-fertilization stage
Carnegie stage 19
18th week post-fertilization stage
22nd week post-fertilization stage
Disease
Normal
Sex
Female
Male
Technology
10x 5' v1
Suspension type
Cell
Related Links
ArrayExpress BioStudies:E-MTAB-11278
ArrayExpress BioStudies:E-MTAB-11267
ArrayExpress BioStudies:E-MTAB-11265
ArrayExpress BioStudies:E-MTAB-11266
Sanger Dataset:fetal-lung
genome.ucsc.edu
Github:Peng-He-Lab/Human_fetal_lung_cell_atlas_2022
CELLxGENE
9,070 cells
•
Yan et al., 2020
Cell Atlas of The Human Fovea and Peripheral Retina
Explore
h5ad
Homo sapiens
Homo sapiens
Retinal cone cell
+1
Retinal cone 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 cone cell
Retinal rod 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
CELLxGENE
9,015 cells
•
Nowicki-Osuch et al., 2023
Single-Cell RNA Sequencing Unifies Developmental Programs of Esophageal and Gastric Intestinal Metaplasia
Explore
h5ad
Homo sapiens
Homo sapiens
Memory b cell
+2
Memory b cell
Esophagogastric junction
+7
Esophagogastric junction
62-year-old stage
+24
62-year-old stage
Gastritis
+3
Gastritis
Female
+1
Female
10x 3' v2
+1
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Memory b cell
Iga plasma cell
Igg plasma cell
Tissue
Esophagogastric junction
Colon
Submucosal esophageal gland
Duodenum
Cardia of stomach
Body of stomach
Rectum
Lower esophagus
Developmental stage
62-year-old stage
43-year-old stage
54-year-old stage
34-year-old stage
42-year-old stage
56-year-old stage
68-year-old stage
55-year-old stage
57-year-old stage
83-year-old stage
77-year-old stage
74-year-old stage
63-year-old stage
48-year-old stage
27-year-old stage
67-year-old stage
80 year-old and over stage
58-year-old stage
50-year-old stage
45-year-old stage
53-year-old stage
29-year-old stage
69-year-old stage
51-year-old stage
41-year-old stage
Disease
Gastritis
Gastric intestinal metaplasia
Barrett esophagus
Normal
Sex
Female
Male
Technology
10x 3' v2
10x 3' v3
Suspension type
Cell
Related Links
EGA dataset:EGAD00001010074
Github:karolno/BE-GIM_Comparison
CELLxGENE
8,982 cells
•
Kumar et al., 2023
A spatially resolved single-cell genomic atlas of the adult human breast
Explore
h5ad
Homo sapiens
Homo sapiens
Endothelial cell of lymphatic vessel
Endothelial cell of lymphatic vessel
Breast
Breast
Adult stage
+1
Adult stage
Normal
Normal
Female
Female
10x 3' v2
+1
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Endothelial cell of lymphatic vessel
Tissue
Breast
Developmental stage
Adult stage
Prime adult stage
Disease
Normal
Sex
Female
Technology
10x 3' v2
10x 3' v3
Suspension type
Cell
Related Links
Github:navinlabcode/HumanBreastCellAtlas
breastatlas.org
GEO series:GSE195665
HumanCellAtlas:1ffa2223-28a6-4133-a5a4-badd00faf4bc
CELLxGENE
8,978 cells
•
Jardine et al., 2021
Blood and immune development in human fetal bone marrow and Down syndrome
Explore
h5ad
Homo sapiens
Homo sapiens
Plasmacytoid dendritic cell
+27
Plasmacytoid dendritic cell
Bone marrow
Bone marrow
Fifth lmp month stage
Fifth lmp month stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Plasmacytoid dendritic cell
Dendritic cell
Endothelial cell of sinusoid
Precursor b cell
Progenitor cell
Naive b cell
Common myeloid progenitor
Neutrophil
Granulocyte monocyte progenitor cell
Pro-b cell
Cd4-positive, alpha-beta t cell
Macrophage
Early lymphoid progenitor
Primitive red blood cell
Erythrocyte
Fraction a pre-pro b cell
Osteoclast
Immature b cell
Megakaryocyte
Endothelial tip cell
Promyelocyte
Cd16-negative, cd56-bright natural killer cell, human
Cd14-positive monocyte
Promonocyte
Basophil
Hematopoietic multipotent progenitor cell
Mast cell
Eosinophil
Tissue
Bone marrow
Developmental stage
Fifth lmp month stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
fbm.cellatlas.io
haniffalab.com
ArrayExpress BioStudies:E-MTAB-9801
ncbi.nlm.nih.gov
HumanCellAtlas:04ad400c-58cb-40a5-bc2b-2279e13a910b
ENA Project:PRJEB41514
ArrayExpress BioStudies:E-MTAB-10042
Single Cell Expression Atlas Experiment:E-CURD-112
Single Cell Expression Atlas Experiment:E-MTAB-9801
Github:haniffalab/FCA_bone_marrow
ArrayExpress BioStudies:E-MTAB-9389
CELLxGENE
8,959 cells
•
Braun et al., 2023
Comprehensive cell atlas of the first-trimester developing human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Erythrocyte
Erythrocyte
Cerebellum
+26
Cerebellum
10th week post-fertilization stage
+11
10th week post-fertilization stage
Normal
Normal
10x 3' v2
+1
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Erythrocyte
Tissue
Cerebellum
Hippocampal formation
Entorhinal cortex
Brain
Caudate-putamen
Upper layers of the cortex
Hindbrain
Midbrain
Pons
Forebrain
Frontal cortex
Head
Lower layers of the cortex
Hypothalamus
Dorsal plus ventral thalamus
Striatum
Telencephalon
Metencephalon
Basal forebrain
Diencephalon
Midbrain tectum
Cerebral subcortex
Medulla oblongata
Occipital cortex
Cortex
Choroid plexus epithelium
Cerebellar peduncular complex
Developmental stage
10th week post-fertilization stage
14th week post-fertilization stage
9th week post-fertilization stage
11th week post-fertilization stage
Carnegie stage 15
Carnegie stage 20
Carnegie stage 16
15th week post-fertilization stage
Carnegie stage 22
Carnegie stage 18
13th week post-fertilization stage
12th week post-fertilization stage
Disease
Normal
Sex
Technology
10x 3' v2
10x 3' v3
Suspension type
Cell
Related Links
EGA dataset:EGAD00001006049
Github:linnarsson-lab/developing-human-brain?tab=readme-ov-file
CELLxGENE
8,945 cells
•
Almanzar et al., 2020
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Explore
h5ad
Mus musculus
Mus musculus
Bladder urothelial cell
+3
Bladder urothelial cell
Bladder lumen
Bladder lumen
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
Bladder urothelial cell
Leukocyte
Bladder cell
Endothelial cell
Tissue
Bladder lumen
Developmental stage
4-week-old stage
20-month-old stage and over
18-month-old stage
3-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
8,863 cells
•
Govek et al., 2022
Combined single-cell RNA-seq profiling and enhancer editing reveals critical spatiotemporal controls over thalamic nuclei formation in the murine embryo
Explore
h5ad
Mus musculus
Mus musculus
Gabaergic neuron
+2
Gabaergic neuron
Diencephalon
Diencephalon
Theiler stage 22
Theiler stage 22
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Mus musculus
Cell type
Gabaergic neuron
Neural progenitor cell
Glutamatergic neuron
Tissue
Diencephalon
Developmental stage
Theiler stage 22
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
CELLxGENE
8,841 cells
•
Mannens et al., 2024
Chromatin accessibility during human first-trimester neurodevelopment
Explore
h5ad
Homo sapiens
Homo sapiens
Pericyte
+2
Pericyte
Cerebellum
+7
Cerebellum
10th week post-fertilization stage
+4
10th week post-fertilization stage
Normal
Normal
Female
+1
Female
10x multiome
10x multiome
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Pericyte
Vascular leptomeningeal cell
Vascular associated smooth muscle cell
Tissue
Cerebellum
Brain
Hindbrain
Midbrain
Pons
Telencephalon
Diencephalon
Medulla oblongata
Developmental stage
10th week post-fertilization stage
9th week post-fertilization stage
13th week post-fertilization stage
12th week post-fertilization stage
Embryonic stage
Disease
Normal
Sex
Female
Male
Technology
10x multiome
Suspension type
Nucleus
Related Links
EGA Study:EGAS00001007472
Github:linnarsson-lab/fetal_brain_multiomics
Single Cell Portal
8,776 cells
Explore
Mus musculus
Mus musculus
Plasmacytoid dendritic cell
+4
Plasmacytoid dendritic cell
Triple-negative breast carcinoma
Triple-negative breast carcinoma
Seq-well s3
Seq-well s3
Organism
Mus musculus
Cell type
Plasmacytoid dendritic cell
Natural killer cell
T cell
Conventional dendritic cell
Myeloid cell
Tissue
Developmental stage
Disease
Triple-negative breast carcinoma
Sex
Technology
Seq-well s3
Suspension type
CELLxGENE
8,753 cells
•
King et al., 2021
Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics
Explore
h5ad
Homo sapiens
Homo sapiens
Natural killer cell
+9
Natural killer cell
Tonsil
Tonsil
3-year-old stage
+3
3-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v2
+1
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Natural killer cell
Innate lymphoid cell
Central memory cd4-positive, alpha-beta t cell
T cell
Regulatory t cell
Central memory cd8-positive, alpha-beta t cell
T follicular regulatory cell
Cd8-positive, alpha-beta cytotoxic t cell
T follicular helper cell
Cd4-positive helper t cell
Tissue
Tonsil
Developmental stage
3-year-old stage
5-year-old stage
6-year-old stage
9-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
10x 5' v1
Suspension type
Cell
Related Links
tonsilimmune.org
ArrayExpress BioStudies:E-MTAB-8999
ArrayExpress BioStudies:E-MTAB-9003
ArrayExpress BioStudies:E-MTAB-9005
HumanCellAtlas:24d0dbbc-54eb-4904-8141-934d26f1c936
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