Pan troglodytes

L6b glutamatergic cortical neuron Myeloid cell Astrocyte Lamp5 gabaergic interneuron Inhibitory interneuron Pvalb chandelier gabaergic interneuron Smooth muscle cell L2/3 intratelencephalic projecting glutamatergic neuron Vip gabaergic interneuron Oligodendrocyte precursor cell Oligodendrocyte B cell L6 corticothalamic-projecting glutamatergic cortical neuron Pericyte Erythroid lineage cell L5/6 near-projecting glutamatergic neuron of the primary motor cortex Pvalb gabaergic interneuron Macrophage Sst gabaergic interneuron L5 extratelencephalic projecting glutamatergic cortical neuron L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex Vascular leptomeningeal cell Microglial cell T cell Endothelial cell

Dorsolateral prefrontal cortex

Prime adult stage

Normal

Female Male

10x 3' v3

Nucleus

Homo sapiens

Fibroblast Keratinocyte Mast cell Neutrophil Malignant cell Plasma cell B cell Chondrocyte Hepatocyte Macrophage Erythrocyte Monocyte Mature nk t cell T cell Endothelial cell

Neck Lung Liver Bone spine Axilla Breast

54-year-old stage 35-year-old stage 53-year-old stage 57-year-old stage 36-year-old stage 52-year-old stage 40-year-old stage 38-year-old stage 41-year-old stage 30-year-old stage 55-year-old stage 58-year-old stage 50-year-old stage 64-year-old stage 29-year-old stage 32-year-old stage 28-year-old stage 60-year-old stage 37-year-old stage 43-year-old stage 44-year-old stage

Breast cancer

Female

10x 3' v3 10x 3' v2

Cell

Homo sapiens

Fibroblast Innate lymphoid cell Perivascular cell Retinal ganglion cell Schwann cell Common myeloid progenitor Neural progenitor cell Retinal cell Mast cell Mesenchyme condensation cell Leptomeningeal cell Neuroblast (sensu vertebrata) Endothelial cell of arteriole Spinal cord radial glial cell Metamyelocyte Vein endothelial cell Choroid plexus macrophage Smooth muscle cell Fibroblast of choroid plexus Oligodendrocyte precursor cell Epithelial cell Dendritic cell B cell Mesenchymal cell Chondrocyte Circulating fibrocyte Megakaryocyte Capillary endothelial cell Erythroid progenitor cell Mesothelial cell of dura mater Pericyte Glioblast (sensu vertebrata) Embryonic blood vessel endothelial progenitor cell Neuronal-restricted precursor Arachnoid barrier cell Interneuron Natural killer cell Platelet Forebrain neuroblast Mucosa-associated lymphoid tissue macrophage Pinealocyte Erythroblast Reticulocyte Tip cell Meningeal macrophage Schwann cell precursor Radial glial cell Perivascular macrophage Monocyte Forebrain radial glial cell Promyelocyte Microglial cell Choroid plexus epithelial cell Mechanoreceptor cell Neuron Neural crest cell Endothelial cell Endothelial cell of artery

Meninx Brain meninx Forebrain meninges

Carnegie stage 20 Carnegie stage 18 10th week post-fertilization stage Carnegie stage 21 Carnegie stage 23 13th week post-fertilization stage 12th week post-fertilization stage 9th week post-fertilization stage Carnegie stage 16

Normal

Female Male

10x 3' v3

Cell

Mus musculus

Fibroblast Olfactory receptor cell Schwann cell Osteoclast Sustentacular cell Neural progenitor cell Ionocyte Mast cell Group 2 innate lymphoid cell Smooth muscle cell Neutrophil Epithelial cell Stromal cell Alpha-beta t cell Plasma cell Oligodendrocyte Dendritic cell B cell Gamma-delta t cell Chondrocyte Tuft cell Pericyte Hematopoietic stem cell Precursor b cell Plasmacytoid dendritic cell Goblet cell Glandular secretory epithelial cell Vomeronasal sensory neuron Cd8-positive, alpha-beta t cell Granulocyte monocyte progenitor cell Natural killer cell Macrophage Ciliated epithelial cell Group 3 innate lymphoid cell Osteoblast Monocyte Basal cell Cd4-positive, alpha-beta t cell Serous secreting cell Endothelial cell

Influenza Normal

10x 3' v3

Homo sapiens

L6b glutamatergic cortical neuron Lamp5 gabaergic interneuron Astrocyte of the cerebral cortex Corticothalamic-projecting glutamatergic cortical neuron Pvalb chandelier gabaergic interneuron Vip gabaergic interneuron Oligodendrocyte precursor cell Caudal ganglionic eminence derived interneuron L2/3-6 intratelencephalic projecting glutamatergic neuron Oligodendrocyte Cerebral cortex endothelial cell Pvalb gabaergic interneuron Sncg gabaergic interneuron Sst gabaergic interneuron L5 extratelencephalic projecting glutamatergic cortical neuron Near-projecting glutamatergic cortical neuron Vascular leptomeningeal cell Microglial cell

Middle temporal gyrus

Adult stage 42-year-old stage 50-year-old stage 29-year-old stage 60-year-old stage 43-year-old stage

Normal

Female Male

Smart-seq v4 10x 3' v3

Nucleus

Homo sapiens

Enteroendocrine cell Glial cell Peripheral nervous system neuron Epithelial cell B cell Mesenchymal cell Chondrocyte Myeloid leukocyte Pericyte Epithelial cell of lung Hepatocyte Intestine goblet cell Ciliated epithelial cell Erythroblast Intestinal epithelial cell Mature nk t cell Basal cell Mesothelial cell Endothelial cell

Stomach Lung Pyloric antrum Liver Ileum Epithelium of trachea Small intestine Body of stomach Esophagus Jejunum Duodenum Colon

21st week post-fertilization stage Embryonic stage 19th week post-fertilization stage 15th week post-fertilization stage 11th week post-fertilization stage 13th week post-fertilization stage 12th week post-fertilization stage 18th week post-fertilization stage 9th week post-fertilization stage 17th week post-fertilization stage

Normal

Female Male

10x 3' v3 10x 3' v2

Cell

Homo sapiens

Astrocyte

Intralaminar nuclear group Primary motor cortex Perirhinal cortex Cerebellar nuclear complex Inferior temporal gyrus Dentate gyrus of hippocampal formation Cerebrocerebellum Primary visual cortex Brodmann (1909) area 35 Ventral anterior nucleus of thalamus Brodmann (1909) area 46 Subthalamic nucleus Globus pallidus Nucleus accumbens Primary somatosensory cortex Midbrain tectum Lateral nuclear group of thalamus Inferior frontal gyrus Epithalamus Cuneus cortex Retrosplenial region Medial dorsal nucleus of thalamus Medial zone of hypothalamus Putamen Lateral geniculate body Brodmann (1909) area 25 Nucleus of medulla oblongata Red nucleus Corticomedial nuclear complex Nucleus of dorsal thalamus Brodmann (1909) area 14 Pontine reticular formation Brodmann (1909) area 19 Midbrain nucleus Piriform cortex Pontine tegmentum Accessory basal amygdaloid nucleus Anterior olfactory nucleus Hypothalamus Granular insular cortex Centromedian nucleus of thalamus Brodmann (1909) area 32 Superior temporal gyrus Substantia nigra Primary auditory cortex Brodmann (1909) area 24 Cerebellar vermis Uncal ca1 Anterior cortical amygdaloid nucleus Lateral entorhinal cortex Septal nuclear complex Basolateral amygdaloid nuclear complex Spinal cord Preoptic area Middle temporal gyrus Parabrachial nucleus Brodmann (1909) area 38 Agranular insular cortex Pulvinar nucleus Body of caudate nucleus Temporal fusiform gyrus Extrastriate cortex Brodmann (1909) area 23 Medial entorhinal cortex Lateral amygdaloid nucleus Supraoptic nucleus Posterior parahippocampal gyrus Pontine nuclear group Median tuberal portion Superior parietal cortex Dorsal tegmental nucleus Substantia innominata Bed nucleus of stria terminalis Brodmann (1909) area 13 Medial geniculate body Inferior olivary complex Gray matter of midbrain Mammillary body Anterior nuclear group Central amygdaloid nucleus Subicular complex Brodmann (1909) area 43 Hippocampal field Rostral ca3 Brodmann (1909) area 40 Claustrum of brain Pretectal region Lateral posterior nucleus of thalamus

42-year-old stage 50-year-old stage 29-year-old stage 60-year-old stage

Normal

Female Male

10x 3' v3

Nucleus

Homo sapiens

Enterocyte Type ec enteroendocrine cell Epithelial cell Type l enteroendocrine cell Tuft cell Paneth cell Goblet cell Stem cell

Ileum lamina propria Ileal epithelium Ileum Small intestine Epithelium of small intestine Lamina propria of small intestine

Third decade stage Sixth decade stage Fourth decade stage Eighth decade stage Fifth decade stage Seventh decade stage

Crohn disease Normal

Female Male

10x 3' v3 10x 3' v2

Cell

Homo sapiens

L6b glutamatergic cortical neuron Lamp5 gabaergic interneuron Astrocyte of the cerebral cortex Corticothalamic-projecting glutamatergic cortical neuron Pvalb chandelier gabaergic interneuron Vip gabaergic interneuron Oligodendrocyte precursor cell Caudal ganglionic eminence derived interneuron L2/3-6 intratelencephalic projecting glutamatergic neuron Oligodendrocyte Cerebral cortex endothelial cell Pvalb gabaergic interneuron Sncg gabaergic interneuron Sst gabaergic interneuron L5 extratelencephalic projecting glutamatergic cortical neuron Near-projecting glutamatergic cortical neuron Vascular leptomeningeal cell Microglial cell

Primary somatosensory cortex

42-year-old stage 50-year-old stage 29-year-old stage 60-year-old stage 43-year-old stage

Normal

Female Male

10x 3' v3

Nucleus

Homo sapiens

Innate lymphoid cell Mast cell Naive t cell Plasma cell Dendritic cell B cell Regulatory t cell Plasmacytoid dendritic cell Leukocyte Cd8-positive, alpha-beta t cell Natural killer cell Macrophage Conventional dendritic cell Monocyte Cd4-positive, alpha-beta t cell T cell

Mucosa of transverse colon Ascending colon Sigmoid colon Colonic epithelium Cecum mucosa Caecum epithelium Descending colon Mucosa of sigmoid colon Lamina propria of mucosa of colon Colon

Adult stage Third decade stage Sixth decade stage Fourth decade stage Eighth decade stage Fifth decade stage Seventh decade stage

Crohn disease Normal

Female Male

10x 3' v3 10x 3' v1 10x 3' v2

Cell

Homo sapiens

Fibroblast Cytotoxic t cell Innate lymphoid cell Helper t cell Schwann cell Endothelial cell of vascular tree Mast cell Melanocyte of skin Smooth muscle cell Plasma cell Basal cell of epidermis Dendritic cell Regulatory t cell Chondrocyte Pericyte Plasmacytoid dendritic cell Cell of skeletal muscle Endothelial cell of lymphatic vessel Natural killer cell Macrophage Suprabasal keratinocyte Conventional dendritic cell Monocyte Basal cell Cd8-positive, alpha-beta memory t cell, cd45ro-positive

Skin of forehead Skin of external ear Arm skin Skin of temple Nose skin Skin of abdomen Skin of cheek

54-year-old stage 90-year-old stage 39-year-old stage 62-year-old stage 27-year-old stage 78-year-old stage 73-year-old stage 53-year-old stage 85-year-old stage 81-year-old stage 86-year-old stage 70-year-old stage 59-year-old stage 23-year-old stage 51-year-old stage 66-year-old stage 77-year-old stage 69-year-old stage 63-year-old stage 80-year-old stage 25-year-old stage 56-year-old stage 91-year-old stage 24-year-old stage

Basal cell carcinoma Normal

Female Male

10x 3' v3 10x 3' v1 10x 3' v2

Cell

Homo sapiens

Neuron

Primary motor cortex Perirhinal cortex Cerebellar nuclear complex Dentate gyrus of hippocampal formation Ventral anterior nucleus of thalamus Globus pallidus Nucleus accumbens Lateral nuclear group of thalamus Putamen Lateral geniculate body Brodmann (1909) area 25 Corticomedial nuclear complex Piriform cortex Accessory basal amygdaloid nucleus Anterior olfactory nucleus Hypothalamus Granular insular cortex Superior temporal gyrus Substantia nigra Primary auditory cortex Brodmann (1909) area 24 Uncal ca1 Anterior cortical amygdaloid nucleus Septal nuclear complex Basolateral amygdaloid nuclear complex Preoptic area Middle temporal gyrus Brodmann (1909) area 38 Agranular insular cortex Pulvinar nucleus Body of caudate nucleus Medial entorhinal cortex Lateral amygdaloid nucleus Supraoptic nucleus Substantia innominata Bed nucleus of stria terminalis Brodmann (1909) area 13 Gray matter of midbrain Mammillary body Anterior nuclear group Central amygdaloid nucleus Hippocampal field Claustrum of brain Pretectal region Lateral posterior nucleus of thalamus

42-year-old stage 50-year-old stage 29-year-old stage 60-year-old stage

Normal

Female Male

10x 3' v3

Nucleus