Homo sapiens

Medial ganglionic eminence derived gabaergic interneuron L2/3 intratelencephalic projecting glutamatergic neuron Glutamatergic neuron Oligodendrocyte precursor cell L5 intratelencephalic projecting glutamatergic neuron Oligodendrocyte Committed oligodendrocyte precursor L4 intratelencephalic projecting glutamatergic neuron Lamp5 gabaergic interneuron Cajal-retzius cell Brain vascular cell Microglial cell Vip gabaergic interneuron Forebrain radial glial cell Immature astrocyte L5 extratelencephalic projecting glutamatergic cortical neuron L6b glutamatergic cortical neuron Pvalb gabaergic interneuron Near-projecting glutamatergic cortical neuron L6 intratelencephalic projecting glutamatergic neuron Intratelencephalic-projecting glutamatergic cortical neuron Caudal ganglionic eminence derived interneuron Sncg gabaergic interneuron Astrocyte Sst gabaergic interneuron Gabaergic neuron Neural progenitor cell Corticothalamic-projecting glutamatergic cortical neuron

Brodmann (1909) area 9 Neocortex Brodmann (1909) area 10 Telencephalon Prefrontal cortex Visual cortex Forebrain Brodmann (1909) area 17

13-year-old stage 21st week post-fertilization stage 13th week post-fertilization stage 3-month-old stage 14th week post-fertilization stage 9-month-old stage 26th week post-fertilization stage 12th week post-fertilization stage 16th week post-fertilization stage 9th week post-fertilization stage Carnegie stage 23 31st week post-fertilization stage 32nd week post-fertilization stage Carnegie stage 21 18th week post-fertilization stage 33rd week post-fertilization stage 5-month-old stage 7-month-old stage 34th week post-fertilization stage 11th week post-fertilization stage

Normal

Female Male

10x multiome

Nucleus

Homo sapiens

B cell

Ulcerative colitis

10x 5' v1

Homo sapiens

Intratelencephalic-projecting glutamatergic cortical neuron

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

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

Normal

Female Male

10x 3' v3

Nucleus

Homo sapiens

Periportal region hepatocyte Hepatocyte Centrilobular region hepatocyte Lymphocyte

Left lobe of liver Right lobe of liver Caudate lobe of liver Liver

37-year-old stage 21-year-old stage 65-year-old stage 26-year-old stage Sixth decade stage 71-year-old stage 53-year-old stage 61-year-old stage 52-year-old stage 54-year-old stage 68-year-old stage 48-year-old stage 39-year-old stage 44-year-old stage 56-year-old stage Fifth decade stage 55-year-old stage 50-year-old stage 80-year-old stage 51-year-old stage 57-year-old stage 72-year-old stage Third decade stage 49-year-old stage Seventh decade stage 58-year-old stage 59-year-old stage Adult stage 67-year-old stage Late adult stage 32-year-old stage 33-year-old stage 64-year-old stage 45-year-old stage 62-year-old stage 41-year-old stage 70-year-old stage 46-year-old stage 60-year-old stage Fourth decade stage Eighth decade stage Prime adult stage Ninth decade stage Young adult stage

Normal

Female Male

10x 5' v1 10x 3' v3 10x 3' v2

Nucleus Cell

Homo sapiens

Transit amplifying cell of small intestine Bladder urothelial cell Progenitor cell of mammary luminal epithelium Club cell Respiratory tract goblet cell Serous cell of epithelium of bronchus Hepatocyte Intestinal crypt stem cell of colon Luminal cell of prostate epithelium Enterocyte of epithelium proper of small intestine Multiciliated columnar cell of tracheobronchial tree Conjunctival epithelial cell Enterochromaffin-like cell Best4+ enterocyte Retinal pigment epithelial cell Interstitial cell of cajal Pulmonary ionocyte Corneal epithelial cell Myo-medullary thymic epithelial cell Pancreatic acinar cell Pancreatic pp cell Blood vessel smooth muscle cell Basal cell Luminal epithelial cell of mammary gland Taste receptor cell Ionocyte Epithelial cell Intestinal tuft cell Pancreatic a cell Enteroendocrine cell Lung multiciliated epithelial cell Vestibular dark cell Enterocyte of epithelium proper of jejunum Myoepithelial cell Ovarian surface epithelial cell Enterocyte of epithelium proper of duodenum Small intestine goblet cell Transit amplifying cell of colon Tuft cell of colon Pancreatic d cell Paneth cell of colon Peritubular myoid cell Neuro-medullary thymic epithelial cell Pulmonary alveolar type 1 cell Paneth cell of epithelium of small intestine Duct epithelial cell Enteroendocrine cell of small intestine Enterocyte of epithelium proper of ileum Acinar cell of salivary gland Type b pancreatic cell Kidney epithelial cell Glandular secretory epithelial cell Acinar cell Medullary thymic epithelial cell Epithelial cell of uterus Mesothelial cell Tracheal goblet cell Supporting cell of vestibular epithelium Ciliated epithelial cell Serous cell of epithelium of trachea Intestinal crypt stem cell of small intestine Mucus secreting cell Pancreatic ductal cell Large intestine goblet cell Enterocyte of epithelium of large intestine Stratified squamous epithelial cell Epithelial fate stem cell Type l enteroendocrine cell Basal cell of prostate epithelium Sebocyte Intrahepatic cholangiocyte Keratocyte Pulmonary alveolar type 2 cell Salivary gland cell

Skin of abdomen Skin of body Lung Ascending colon Heart right ventricle Thymus Conjunctiva Stomach Testis Duodenum Crista ampullaris Uterus Small intestine Anterior part of tongue Utricle of membranous labyrinth Exocrine pancreas Mucosa of stomach Left ovary Trachea Endometrium Cornea Sublingual gland Ileum Liver Endocrine pancreas Ovary Muscle of pelvic diaphragm Stomach smooth muscle Chorioretinal region Anterior segment of eyeball Cardiac ventricle Kidney Eye Right ovary Cardiac atrium Buccal mucosa Heart Tongue Sclera Submandibular gland Mammary gland Jejunum Myometrium Posterior segment of eyeball Large intestine Eyelid Muscle of abdomen Cortex of kidney Parotid gland Ocular surface region Lacrimal gland Posterior part of tongue Bladder organ Skin of chest Sigmoid colon Prostate gland

69-year-old stage 37-year-old stage 26-year-old stage 61-year-old stage 38-year-old stage 56-year-old stage 55-year-old stage 57-year-old stage 74-year-old stage 59-year-old stage 67-year-old stage 33-year-old stage 45-year-old stage 46-year-old stage 60-year-old stage 36-year-old stage 40-year-old stage

Normal

Female Male

10x 5' v2 Smart-seq2 10x 3' v3

Cell

Mus musculus

Osteoblast Muscle cell Natural killer cell Endothelial cell of lymphatic vessel Erythroid progenitor cell Erythrocyte Fibroblast of dermis Mast cell Peridermal cell Hypertrophic chondrocyte Tendon cell Basal cell Endothelial cell of artery Schwann cell Melanocyte Smooth muscle cell Epithelial cell Primitive red blood cell Chondroblast Macrophage Innate lymphoid cell Myelocyte Type 1 submucosal plexus glia Onychocyte Common myeloid progenitor Vein endothelial cell Mesenchymal cell Megakaryocyte Skeletal muscle myoblast Myoblast B cell Pericyte Monocyte Myofibroblast cell Basophil Conventional dendritic cell Hair follicle melanocyte Fibroblast Schwann cell precursor Chondrocyte Muscle fibroblast

Hindlimb Forelimb

Theiler stage 22 Theiler stage 24 Theiler stage 18 Theiler stage 16 Theiler stage 19 Theiler stage 26 Theiler stage 20 Theiler stage 21 Theiler stage 23

Normal

10x 3' v3 10x 3' v2

Cell

Homo sapiens

Cycling t cell Blood vessel endothelial cell Natural killer cell Endothelial cell of lymphatic vessel Mast cell Cd8-positive, alpha-beta t cell Plasmacytoid dendritic cell, human Macrophage Cd4-positive, cd25-positive, alpha-beta regulatory t cell Myeloid cell Plasma cell Salivary gland glandular cell Squamous epithelial cell T follicular helper cell B cell Pericyte Naive thymus-derived cd4-positive, alpha-beta t cell Monocyte Conventional dendritic cell Fibroblast

Gingiva of lower jaw Hypopharynx Buccal mucosa Alveolar ridge of mandible Larynx Mandible Tongue Oropharynx Oral cavity Mouth floor

66-year-old stage 69-year-old stage 75-year-old stage 65-year-old stage 43-year-old stage 53-year-old stage 61-year-old stage 54-year-old stage 48-year-old stage 56-year-old stage 55-year-old stage 50-year-old stage 80-year-old stage 51-year-old stage 57-year-old stage 72-year-old stage 74-year-old stage 35-year-old stage 58-year-old stage 67-year-old stage 32-year-old stage 77-year-old stage 64-year-old stage 45-year-old stage 62-year-old stage 70-year-old stage 60-year-old stage 18-year-old stage 73-year-old stage

Head and neck squamous cell carcinoma

Female Male

10x 5' transcription profiling 10x 3' v3 10x 3' v2

Cell

Homo sapiens

Caudal ganglionic eminence derived interneuron

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

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

Normal

Female Male

10x 3' v3

Nucleus

Homo sapiens

Diffuse bipolar 1 cell Diffuse bipolar 4 cell Gabaergic amacrine cell Diffuse bipolar 2 cell Retinal ganglion cell Off parasol ganglion cell Offx cell On-bipolar cell Rod bipolar cell S cone cell On parasol ganglion cell Invaginating midget bipolar cell Retinal bipolar neuron H2 horizontal cell Retinal cone cell Glycinergic amacrine cell Retinal rod cell Flat midget bipolar cell Retina horizontal cell Amacrine cell Diffuse bipolar 3a cell Retinal progenitor cell Starburst amacrine cell Midget ganglion cell of retina Diffuse bipolar 6 cell Mueller cell H1 horizontal cell Diffuse bipolar 3b cell

Peripheral region of retina Macula lutea Retina

21st week post-fertilization stage 13th week post-fertilization stage 14th week post-fertilization stage 15th week post-fertilization stage 20th week post-fertilization stage 17th week post-fertilization stage 12th week post-fertilization stage 9th week post-fertilization stage 24th week post-fertilization stage 11th week post-fertilization stage

Normal

10x multiome

Nucleus

Homo sapiens

T cell Peyer's patch macrophage Cd1c-positive myeloid dendritic cell Natural killer cell Endothelial cell of lymphatic vessel Gamma-delta t cell Endothelial cell Cd141-positive myeloid dendritic cell Group 2 innate lymphoid cell Classical monocyte Plasmacytoid dendritic cell Precursor b cell Cd8-positive, alpha-beta memory t cell Group 3 innate lymphoid cell Naive thymus-derived cd8-positive, alpha-beta t cell Macrophage Regulatory t cell Mural cell Plasma cell Cd4-positive, alpha-beta memory t cell Naive thymus-derived cd4-positive, alpha-beta t cell Mucosal invariant t cell Cd34-negative, cd117-positive innate lymphoid cell, human Naive b cell Fibroblast Dendritic cell

Synovial fluid Blood Layer of synovial tissue

Pediatric stage 2-year-old stage 15-year-old stage 9-year-old stage 14-year-old stage 3-year-old stage 7-year-old stage 10-year-old stage 4-year-old stage

Juvenile idiopathic arthritis

Female Male

10x 5' v2 10x 3' v3

Cell

Homo sapiens

Classical monocyte Plasmacytoid dendritic cell Macrophage Conventional dendritic cell Non-classical monocyte

Lung Inguinal lymph node Jejunal epithelium Epithelial lining fluid Thoracic lymph node Spleen Jejunum lamina propria Blood Bone marrow Mesenteric lymph node

75-year-old stage Sixth decade stage 68-year-old stage 48-year-old stage 56-year-old stage Fifth decade stage Third decade stage 23-year-old stage 25-year-old stage 67-year-old stage 33-year-old stage 64-year-old stage Fourth decade stage 20-year-old stage Eighth decade stage 73-year-old stage 27-year-old stage

Normal

Female Male

10x 5' v2 10x 3' v3

Cell

Homo sapiens

T cell Podocyte Natural killer cell Parietal epithelial cell Kidney interstitial alternatively activated macrophage Cytotoxic t cell Endothelial cell Kidney loop of henle thin descending limb epithelial cell Mature nk t cell Mast cell Kidney collecting duct intercalated cell Epithelial cell of proximal tubule Plasmacytoid dendritic cell, human Kidney distal convoluted tubule epithelial cell Kidney collecting duct principal cell Kidney connecting tubule epithelial cell Kidney loop of henle thick ascending limb epithelial cell Kidney interstitial cell Plasma cell B cell Monocyte Kidney loop of henle thin ascending limb epithelial cell Conventional dendritic cell Non-classical monocyte Mononuclear phagocyte

Kidney

66-year-old stage 42-year-old stage Sixth decade stage 53-year-old stage 52-year-old stage 48-year-old stage 30-year-old stage 39-year-old stage 56-year-old stage Fifth decade stage 57-year-old stage Third decade stage 49-year-old stage 35-year-old stage Seventh decade stage 41-year-old stage 31-year-old stage Fourth decade stage Eighth decade stage 47-year-old stage Ninth decade stage 40-year-old stage

Chronic kidney disease Normal Acute kidney failure

Female Male

10x 3' v3

Cell