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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
4,837 cells
•
Bakken et al., 2021
Comparative cellular analysis of motor cortex in human, marmoset and mouse
Explore
h5ad
Macaca mulatta
Macaca mulatta
Glutamatergic neuron
Glutamatergic neuron
Primary motor cortex
Primary motor cortex
Post-juvenile adult stage
Post-juvenile adult stage
Normal
Normal
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Macaca mulatta
Cell type
Glutamatergic neuron
Tissue
Primary motor cortex
Developmental stage
Post-juvenile adult stage
Disease
Normal
Sex
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
Github:AllenInstitute/scrattch.hicat
protocols.io:human-tissue-slicing-and-dissections-for-nuclear-i-dm6gpre85vzp
nemoanalytics.org
protocols.io:isolation-of-nuclei-from-adult-human-brain-tissue-eq2lyd1nqlx9/v2
Github:broadinstitute/Drop-seq
viewer.cytosplore.org
nemoanalytics.org
protocols.io:preparation-of-frozen-nuclei-for-single-nucleus-rn-eq2lyrdpgx9k/v1
NeMo archive:dat-ek5dbmu
protocols.io:isolation-of-nuclei-from-adult-human-brain-tissue-j8nlk56k1l5r/v1
Github:AllenInstitute/BICCN_M1_Evo
protocols.io:extraction-of-nuclei-from-brain-tissue-2srged6
CELLxGENE
4,792 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
Neutrophil
+6
Neutrophil
Blood
Blood
66-year-old stage
66-year-old stage
Covid-19
Covid-19
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Neutrophil
Mature nk t cell
Platelet
Myeloid cell
Plasma cell
B cell
Dendritic cell
Tissue
Blood
Developmental stage
66-year-old stage
Disease
Covid-19
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
Github:simslab/cluster_diffex2018
COVID-19 cell atlas
Mendeley Data Dataset:fm7v43jrbk/2
CELLxGENE
4,778 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
T cell
+13
T cell
Lung
Lung
Carnegie stage 19
+6
Carnegie stage 19
Normal
Normal
Female
+1
Female
10x 5' v1
10x 5' v1
Cell
Cell
Organism
Homo sapiens
Cell type
T cell
Natural killer cell
Cd8-positive, alpha-beta t cell
Group 2 innate lymphoid cell
Group 3 innate lymphoid cell
Thymocyte
T-helper 17 cell
Cd16-positive, cd56-dim natural killer cell, human
Regulatory t cell
Type ii nk t cell
Type i nk t cell
Cd4-positive, alpha-beta memory t cell
Cd16-negative, cd56-bright natural killer cell, human
Cd34-positive, cd56-positive, cd117-positive common innate lymphoid precursor, human
Tissue
Lung
Developmental stage
Carnegie stage 19
15th week post-fertilization stage
20th week post-fertilization stage
9th week post-fertilization stage
18th week post-fertilization stage
22nd week post-fertilization stage
11th 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-11265
ArrayExpress BioStudies:E-MTAB-11266
Sanger Dataset:fetal-lung
genome.ucsc.edu
Github:Peng-He-Lab/Human_fetal_lung_cell_atlas_2022
ArrayExpress BioStudies:E-MTAB-11267
CELLxGENE
4,755 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
Mature nk t cell
+5
Mature nk t cell
Blood
Blood
74-year-old stage
74-year-old stage
Covid-19
Covid-19
Female
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Mature nk t cell
Platelet
Myeloid cell
Plasma cell
B cell
Dendritic cell
Tissue
Blood
Developmental stage
74-year-old stage
Disease
Covid-19
Sex
Female
Technology
10x 3' v3
Suspension type
Cell
Related Links
COVID-19 cell atlas
Mendeley Data Dataset:fm7v43jrbk/2
Github:simslab/cluster_diffex2018
CELLxGENE
4,745 cells
•
Bakken et al., 2021
Comparative cellular analysis of motor cortex in human, marmoset and mouse
Explore
h5ad
Mus musculus
Mus musculus
Oligodendrocyte precursor cell
+7
Oligodendrocyte precursor cell
Primary motor cortex
Primary motor cortex
Prime adult stage
Prime adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Mus musculus
Cell type
Oligodendrocyte precursor cell
Endothelial cell
Oligodendrocyte
Smooth muscle cell
Microglial cell
Leptomeningeal cell
Pericyte
Astrocyte
Tissue
Primary motor cortex
Developmental stage
Prime adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
nemoanalytics.org
protocols.io:isolation-of-nuclei-from-adult-human-brain-tissue-eq2lyd1nqlx9/v2
Github:broadinstitute/Drop-seq
viewer.cytosplore.org
nemoanalytics.org
Github:AllenInstitute/BICCN_M1_Evo
Github:AllenInstitute/scrattch.hicat
NeMo archive:dat-ek5dbmu
protocols.io:extraction-of-nuclei-from-brain-tissue-2srged6
protocols.io:isolation-of-nuclei-from-adult-human-brain-tissue-j8nlk56k1l5r/v1
protocols.io:human-tissue-slicing-and-dissections-for-nuclear-i-dm6gpre85vzp
protocols.io:preparation-of-frozen-nuclei-for-single-nucleus-rn-eq2lyrdpgx9k/v1
CELLxGENE
4,742 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
+8
T cell
Liver
Liver
57-year-old stage
57-year-old stage
Breast cancer
Breast cancer
Female
Female
10x 3' v2
10x 3' v2
Cell
Cell
Organism
Homo sapiens
Cell type
T cell
Hepatocyte
Endothelial cell
Mature nk t cell
Macrophage
Malignant cell
B cell
Monocyte
Fibroblast
Tissue
Liver
Developmental stage
57-year-old stage
Disease
Breast cancer
Sex
Female
Technology
10x 3' v2
Suspension type
Cell
Related Links
humantumoratlas.org
dbGaP Study:phs002371
CELLxGENE
4,723 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
+15
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
Neurectodermal 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
figshare.com
FigShare Dataset:E8_5_Embryo2_h5ad/21695849/1
FigShare Dataset:E9_0_Embryo_h5ad/21695879/1
GEO series:GSE197353
CELLxGENE
4,720 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Committed oligodendrocyte precursor
Committed oligodendrocyte precursor
Brodmann (1909) area 13
+87
Brodmann (1909) area 13
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
Committed oligodendrocyte precursor
Tissue
Brodmann (1909) area 13
Brodmann (1909) area 14
Brodmann (1909) area 19
Brodmann (1909) area 23
Brodmann (1909) area 24
Brodmann (1909) area 25
Brodmann (1909) area 32
Brodmann (1909) area 35
Brodmann (1909) area 38
Brodmann (1909) area 40
Brodmann (1909) area 43
Brodmann (1909) area 46
Accessory basal amygdaloid nucleus
Agranular insular cortex
Anterior cortical amygdaloid nucleus
Anterior nuclear group
Anterior olfactory nucleus
Basolateral amygdaloid nuclear complex
Bed nucleus of stria terminalis
Body of caudate nucleus
Central amygdaloid nucleus
Centromedian nucleus of thalamus
Cerebellar nuclear complex
Cerebellar vermis
Cerebrocerebellum
Claustrum of brain
Corticomedial nuclear complex
Cuneus cortex
Dentate gyrus of hippocampal formation
Dorsal tegmental nucleus
Epithalamus
Extrastriate cortex
Globus pallidus
Granular insular cortex
Gray matter of midbrain
Hippocampal field
Hypothalamus
Inferior frontal gyrus
Inferior olivary complex
Inferior temporal gyrus
Intralaminar nuclear group
Lateral amygdaloid nucleus
Lateral entorhinal cortex
Lateral geniculate body
Lateral nuclear group of thalamus
Lateral posterior nucleus of thalamus
Mammillary body
Medial dorsal nucleus of thalamus
Medial entorhinal cortex
Medial geniculate body
Medial zone of hypothalamus
Median tuberal portion
Midbrain nucleus
Midbrain tectum
Middle temporal gyrus
Nucleus accumbens
Nucleus of dorsal thalamus
Nucleus of medulla oblongata
Parabrachial nucleus
Perirhinal cortex
Piriform cortex
Pontine nuclear group
Pontine reticular formation
Pontine tegmentum
Posterior parahippocampal gyrus
Preoptic area
Pretectal region
Primary auditory cortex
Primary motor cortex
Primary somatosensory cortex
Primary visual cortex
Pulvinar nucleus
Putamen
Red nucleus
Retrosplenial region
Rostral ca3
Septal nuclear complex
Spinal cord
Subicular complex
Substantia innominata
Substantia nigra
Subthalamic nucleus
Superior parietal cortex
Superior temporal gyrus
Supraoptic nucleus
Temporal fusiform gyrus
Uncal ca1
Ventral anterior nucleus of thalamus
Developmental stage
42-year-old stage
29-year-old stage
50-year-old stage
60-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
4,714 cells
•
Siletti et al., 2023
Transcriptomic diversity of cell types across the adult human brain
Explore
h5ad
Homo sapiens
Homo sapiens
Midbrain-derived inhibitory neuron
+22
Midbrain-derived inhibitory neuron
Red nucleus
Red nucleus
29-year-old stage
29-year-old stage
Normal
Normal
Male
Male
10x 3' v3
10x 3' v3
Nucleus
Nucleus
Organism
Homo sapiens
Cell type
Midbrain-derived inhibitory neuron
T cell
Central nervous system macrophage
Natural killer cell
Oligodendrocyte precursor cell
Endothelial cell
Oligodendrocyte
Committed oligodendrocyte precursor
Cerebellar granule cell
Pvalb chandelier gabaergic interneuron
Medial ganglionic eminence derived interneuron
Cerebellar inhibitory gabaergic interneuron
Microglial cell
Bergmann glial cell
Pericyte
Cerebral cortex neuron
Neuron
Monocyte
Intratelencephalic-projecting glutamatergic cortical neuron
Caudal ganglionic eminence derived interneuron
Vascular associated smooth muscle cell
Astrocyte
Fibroblast
Tissue
Red nucleus
Developmental stage
29-year-old stage
Disease
Normal
Sex
Male
Technology
10x 3' v3
Suspension type
Nucleus
Related Links
Github:linnarsson-lab/adult-human-brain
Github:linnarsson-lab/auto-annotation-ah
NeMo archive:biccn/grant/u01_lein/linnarsson/transcriptome/sncell/10x_v3/human/raw
CELLxGENE
4,683 cells
•
Johansen et al., 2023
Interindividual variation in human cortical cell type abundance and expression
Explore
h5ad
Homo sapiens
Homo sapiens
Lamp5 gabaergic interneuron
Lamp5 gabaergic interneuron
Neocortex
Neocortex
Adult stage
Adult stage
Normal
Normal
Female
+1
Female
10x 3' v3
10x 3' v3
Cell
Cell
Organism
Homo sapiens
Cell type
Lamp5 gabaergic interneuron
Tissue
Neocortex
Developmental stage
Adult stage
Disease
Normal
Sex
Female
Male
Technology
10x 3' v3
Suspension type
Cell
Related Links
knowledge.brain-map.org
Allen Brain Map Atlases:rnaseq/human-mtg-10x_sea-ad
NeMo archive:dat-p3eei0g
Github:AllenInstitute/human_variation
Allen Brain Map:classes/multimodal-characterization
CELLxGENE
4,667 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
+15
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
Neurectodermal 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
Bgee
4,661 cells
•
Guo et al., 2019
The Cellular Diversity and Transcription Factor Code of Drosophila Enteroendocrine Cells
Explore
scRNA-Seq droplet-based processed expression values per cell population in Drosophila melanogaster (tsv.gz)
scRNA-Seq droplet-based H5AD data per cell in Drosophila melanogaster (h5ad)
Drosophila melanogaster
Drosophila melanogaster
Adult enteroendocrine precursor cell
+8
Adult enteroendocrine precursor cell
Adult midgut
Adult midgut
Mature adult stage
Mature adult stage
Normal
Normal
Female
Female
10x genomics v2
10x genomics v2
Organism
Drosophila melanogaster
Cell type
Adult enteroendocrine precursor cell
Adult anterior midgut class i enteroendocrine cell
Adult anterior midgut class ii enteroendocrine cell
Adult class iii enteroendocrine cell
Adult class i enteroendocrine cell
Adult middle midgut class ii enteroendocrine cell
Adult posterior midgut class ii enteroendocrine cell
Adult posterior midgut class i enteroendocrine cell
Adult middle midgut class i enteroendocrine cell
Tissue
Adult midgut
Developmental stage
Mature adult stage
Disease
Normal
Sex
Female
Technology
10x genomics v2
Suspension type
Related Links
SRA Project:SRP200614
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