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Tissue
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Disease
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Sex
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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
10,729 cells
•
Garcia-Alonso et al., 2021
Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro
Explore
h5ad
Homo sapiens
Homo sapiens
Glandular secretory epithelial cell
+2
Glandular secretory epithelial cell
Endometrium
Endometrium
26-year-old stage
+4
26-year-old stage
Normal
Normal
Female
Female
10x 3' v2
+1
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
Glandular secretory epithelial cell
Ciliated cell
Epithelial cell
Tissue
Endometrium
Developmental stage
26-year-old stage
Young adult stage
Third decade stage
29-year-old stage
37-year-old stage
Disease
Normal
Sex
Female
Technology
10x 3' v2
10x 3' v3
Suspension type
Cell
Related Links
reproductivecellatlas.org
ArrayExpress BioStudies:E-MTAB-9260
ArrayExpress BioStudies:E-MTAB-10283
EGA dataset:EGAD00001007909
HumanCellAtlas:2b38025d-a5ea-4c0f-b22e-367824bcaf4c
ArrayExpress BioStudies:E-MTAB-10287
CELLxGENE
10,701 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
+13
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
Macula densa 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
CELLxGENE
10,696 cells
•
Chen et al., 2021
Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps
Explore
h5ad
Homo sapiens
Homo sapiens
T cell
+6
T cell
Ascending colon
+6
Ascending colon
62-year-old stage
+26
62-year-old stage
Tubular adenoma
+5
Tubular adenoma
Female
+1
Female
Trudrop
Trudrop
Cell
Cell
Organism
Homo sapiens
Cell type
T cell
B cell
Endothelial cell
Fibroblast
Plasma cell
Mast cell
Myeloid cell
Tissue
Ascending colon
Hepatic cecum
Descending colon
Sigmoid colon
Hepatic flexure of colon
Transverse colon
Rectum
Developmental stage
62-year-old stage
66-year-old stage
54-year-old stage
59-year-old stage
64-year-old stage
46-year-old stage
56-year-old stage
68-year-old stage
55-year-old stage
57-year-old stage
60-year-old stage
74-year-old stage
63-year-old stage
76-year-old stage
72-year-old stage
67-year-old stage
52-year-old stage
58-year-old stage
65-year-old stage
50-year-old stage
53-year-old stage
69-year-old stage
73-year-old stage
51-year-old stage
70-year-old stage
40-year-old stage
71-year-old stage
Disease
Tubular adenoma
Colon sessile serrated adenoma/polyp
Hyperplastic polyp
Tubulovillous adenoma
Colorectal cancer
Normal
Sex
Female
Male
Technology
Trudrop
Suspension type
Cell
Related Links
HumanCellAtlas:50154d1e-2308-44bf-9608-10c7afaa560b
dbGaP Study:phs002371
humantumoratlas.org
CELLxGENE
10,689 cells
•
Dong et al., 2024
Transcriptome Analysis of Archived Tumor Tissues by Visium, GeoMx DSP, and Chromium Methods Reveals Inter- and Intra-Patient Heterogeneity
Explore
h5ad
Homo sapiens
Homo sapiens
Activated cd8-positive, alpha-beta t cell
+18
Activated cd8-positive, alpha-beta t cell
Parenchyma of mammary gland
Parenchyma of mammary gland
Adult stage
Adult stage
Invasive ductal breast carcinoma
+1
Invasive ductal breast carcinoma
Female
Female
10x gene expression flex
10x gene expression flex
Cell
Cell
Organism
Homo sapiens
Cell type
Activated cd8-positive, alpha-beta t cell
Plasmacytoid dendritic cell
Natural killer cell
Cd4-positive, alpha-beta memory t cell
Pericyte
Conventional dendritic cell
Natural t-regulatory cell
Classical monocyte
Malignant cell
Fibroblast of lung
Smooth muscle cell
Macrophage
Dendritic cell, human
Granulocyte
Capillary endothelial cell
Plasma cell
Mast cell
Cytotoxic t cell
Fibroblast of breast
Tissue
Parenchyma of mammary gland
Developmental stage
Adult stage
Disease
Invasive ductal breast carcinoma
Invasive lobular breast carcinoma
Sex
Female
Technology
10x gene expression flex
Suspension type
Cell
Related Links
ArrayExpress BioStudies:E-MTAB-14560
Github:bdsc-tds/mosaic_pilot_study
ArrayExpress BioStudies:E-MTAB-14566
ASAP
10,686 cells
•
Li et al., 2022
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly
Explore
h5ad
Drosophila melanogaster
Drosophila melanogaster
Adult neuron
+7
Adult neuron
Heart
Heart
Day 5 of adulthood
Day 5 of adulthood
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Organism
Drosophila melanogaster
Cell type
Adult neuron
Embryonic/larval crystal cell
Epithelial cell
Adult pericardial cell
Hemocyte
Sensory neuron
Indirect flight muscle cell
Adult heart ventral longitudinal muscle cell
Tissue
Heart
Developmental stage
Day 5 of adulthood
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Related Links
ArrayExpress BioStudies:E-MTAB-10519
CELLxGENE
10,654 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Hippocampal ca4 neuron
Hippocampal ca4 neuron
Substantia nigra
+9
Substantia nigra
42-year-old stage
+3
42-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Hippocampal ca4 neuron
Tissue
Substantia nigra
Hippocampal field
Rostral ca3
Uncal ca1
Bed nucleus of stria terminalis
Primary motor cortex
Retrosplenial region
Pulvinar nucleus
Dentate gyrus of hippocampal formation
Septal nuclear complex
Developmental stage
42-year-old stage
60-year-old stage
50-year-old stage
29-year-old stage
Disease
Normal
Sex
Female
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
10,623 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
T cell
+5
T cell
Axilla
Axilla
37-year-old stage
37-year-old stage
Breast cancer
Breast cancer
Female
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
T cell
Malignant cell
Macrophage
Blood vessel smooth muscle cell
Blood vessel endothelial cell
Fibroblast
Tissue
Axilla
Developmental stage
37-year-old stage
Disease
Breast cancer
Sex
Female
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
humantumoratlas.org
dbGaP Study:phs002371
CELLxGENE
10,536 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
Goblet cell
+3
Goblet cell
Multicellular anatomical structure
+3
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
Goblet cell
Nonkeratinized cell of epidermis
Epidermal mucus secreting cell
Ionocyte
Tissue
Multicellular anatomical structure
Taste bud
Integument
Ectoderm-derived 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
cole-trapnelllab.github.io
DOI:10.1038/s41586-023-06720-2
GEO series:GSE295164
CELLxGENE
10,533 cells
•
Mimpen et al., 2024
Single nucleus and spatial transcriptomic profiling of healthy human hamstring tendon
Explore
h5ad
Homo sapiens
Homo sapiens
Skeletal muscle satellite cell
+10
Skeletal muscle satellite cell
Tendon of semitendinosus
Tendon of semitendinosus
18-year-old stage
+3
18-year-old stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Skeletal muscle satellite cell
Leukocyte
Neural cell
Endothelial cell of lymphatic vessel
Skeletal muscle fiber
Mural cell
Endothelial cell of vascular tree
Slow muscle cell
Adipocyte
Fast muscle cell
Fibroblast
Tissue
Tendon of semitendinosus
Developmental stage
18-year-old stage
24-year-old stage
26-year-old stage
37-year-old stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
HumanCellAtlas:838d4660-3d62-4b08-b32d-dc5cbd93919d
Github:Botnar-MSK-Atlas/hamstring_atlas
CELLxGENE
10,459 cells
•
Suo et al., 2022
Mapping the developing human immune system across organs
Explore
h5ad
Homo sapiens
Homo sapiens
Natural killer cell
+6
Natural killer cell
Thymus
Thymus
Normal
Normal
10x 5' v1
10x 5' v1
Cell
Cell
Organism
Homo sapiens
Cell type
Natural killer cell
T cell
Erythrocyte
Group 3 innate lymphoid cell
Thymocyte
Mast cell
Double-positive, alpha-beta thymocyte
Tissue
Thymus
Developmental stage
Disease
Normal
Sex
Technology
10x 5' v1
Suspension type
Cell
Related Links
Human Cell Atlas Developmental:fetal-immune
Teichmann lab
UCSC Cell Browser:fetal-immune
Github:Teichlab/Pan_fetal_immune
DOI:10.1016/j.stem.2018.12.011
HumanCellAtlas:fcaa53cd-ba57-4bfe-af9c-eaa958f95c1a
ArrayExpress BioStudies:E-MTAB-11341
ArrayExpress BioStudies:E-MTAB-11343
BroadInstitute Single-Cell Portal:SCP1843
CELLxGENE
10,419 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
+15
Kidney loop of henle thick ascending limb epithelial cell
Cortex of kidney
Cortex of kidney
75-year-old stage
75-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 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
Kidney collecting duct intercalated cell
Mesangial cell
Kidney connecting tubule epithelial cell
Kidney distal convoluted tubule epithelial cell
Tissue
Cortex of kidney
Developmental stage
75-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
10,411 cells
•
Garcia-Alonso et al., 2022
Single-cell roadmap of human gonadal development
Explore
h5ad
Mus musculus
Mus musculus
Oocyte
+4
Oocyte
Mesoderm
+5
Mesoderm
Theiler stage 21
+8
Theiler stage 21
Normal
Normal
Female
+1
Female
10x 3' v2
+2
10x 3' v2
Cell
Cell
Organism
Mus musculus
Cell type
Oocyte
Male germ cell
Female germ cell
Primordial germ cell
Oogonial cell
Tissue
Mesoderm
Testis
Mesonephros
Gonad primordium
Ovary
Gonad
Developmental stage
Theiler stage 21
Theiler stage 27
Theiler stage 20
5-day-old stage
Theiler stage 26
Theiler stage 19
Theiler stage 22
Theiler stage 24
Theiler stage 17
Disease
Normal
Sex
Female
Male
Technology
10x 3' v2
10x 5' v1
10x 3' v3
Suspension type
Cell
Related Links
ArrayExpress BioStudies:E-MTAB-10551
ArrayExpress BioStudies:E-MTAB-11480
reproductivecellatlas.org
ventolab.org
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