Mus musculus

Endothelial cell of hepatic sinusoid T cell Osteoblast Bladder urothelial cell Podocyte Brown adipocyte Endocardial cell Club cell Granulocyte Respiratory tract goblet cell Hypothalamus cell Hepatocyte Central nervous system macrophage Intestine goblet cell Conjunctiva goblet cell Type i cell of adrenal cortex Ciliated cell Natural killer cell Epithelial cell of parathyroid gland Endothelial cell of lymphatic vessel Erythroid progenitor cell Glutamatergic neuron Oligodendrocyte precursor cell Gingival epithelial cell Spinal cord motor neuron Glomerular endothelial cell Myotube Olfactory epithelial cell Endothelial cell Endo-epithelial cell Kupffer cell Intermediate mesodermal cell Retinal ganglion cell Retinal pigment epithelial cell Microvascular endothelial cell Epithelial cell of pancreas Committed oligodendrocyte precursor Mast cell Adipose macrophage Corneal epithelial cell Pancreatic acinar cell Efferent neuron Ectodermal cell Enteric neuron Auditory epithelial cell Kidney collecting duct intercalated cell Metanephric mesenchyme stem cell Epithelial cell of amnion Peripheral nervous system neuron Sympathetic neuron Endothelial cell of artery Melanocyte Ureteric bud cell Notochordal cell Epithelial cell of proximal tubule Epithelial cell Cerebral cortex gabaergic interneuron Plasmacytoid dendritic cell Neural cell Muscle precursor cell Spiral ganglion neuron Olfactory receptor cell Cajal-retzius cell Brain pericyte Epithelial cell of thyroid gland Mesodermal cell Brown preadipocyte Adipocyte Splanchnic mesodermal cell Retinal bipolar neuron Lateral mesodermal cell Photoreceptor cell Ependymal cell Microglial cell Kidney distal convoluted tubule epithelial cell Kidney collecting duct principal cell Cranial motor neuron Kidney connecting tubule epithelial cell Regulatory t cell Retinal cone cell Extraembryonic cell Pulmonary alveolar type 1 cell Retinal rod cell Lung endothelial cell Embryonic blood vessel endothelial progenitor cell Intestinal enteroendocrine cell Pinealocyte Keratinocyte Small bistratified retinal ganglion cell Pituitary gland cell Hematopoietic stem cell Myeloid suppressor cell Vein endothelial cell Kidney epithelial cell Olfactory ensheathing cell Retina horizontal cell Lens epithelial cell Parasympathetic neuron Cochlea auditory hair cell Megakaryocyte Amacrine cell Retinal progenitor cell Myoblast Thalamic excitatory neuron Choroid plexus epithelial cell Starburst amacrine cell Cardiac muscle cell Perineuronal satellite cell B cell Pericyte Activated cd4-negative, cd8-negative type i nk t cell Neuron Iris pigment epithelial cell Monocyte Cerebral cortex endothelial cell Purkinje cell Kidney loop of henle ascending limb epithelial cell Myofibroblast cell Primitive erythroid progenitor Leydig cell Astrocyte Epithelial cell of thymus Conventional dendritic cell Sensory neuron of dorsal root ganglion Fibroblast Myelinating schwann cell Osteoclast Primordial germ cell Gabaergic neuron Intrahepatic cholangiocyte Pulmonary alveolar type 2 cell Neural progenitor cell Schwann cell precursor Chondrocyte

Embryo

Theiler stage 22 Theiler stage 27 Theiler stage 24 Theiler stage 18 Theiler stage 25 Theiler stage 14 Theiler stage 16 Theiler stage 17 Theiler stage 15 Theiler stage 19 Theiler stage 26 Theiler stage 13 Theiler stage 20 Theiler stage 12 Theiler stage 21 Theiler stage 23

Normal

Female Male

Sci-rna-seq3

Nucleus

Homo sapiens

T cell Glutamatergic neuron Oligodendrocyte precursor cell Oligodendrocyte Matrix d1 medium spiny neuron Capillary endothelial cell Cerebellar golgi cell Smooth muscle cell Dopaminergic neuron Pvalb chandelier gabaergic interneuron Lamp5 gabaergic interneuron Ependymal cell Microglial cell Vip gabaergic interneuron Granule cell Molecular layer interneuron Matrix d2 medium spiny neuron Pvalb gabaergic interneuron Bergmann glial cell Pericyte Perivascular macrophage Purkinje cell Astrocyte Fibroblast Sst gabaergic interneuron Gabaergic neuron Medium spiny neuron

Middle temporal gyrus Cingulate gyrus Substantia nigra Cerebellum Putamen

69-year-old stage 75-year-old stage 89-year-old stage 87-year-old stage 71-year-old stage 85-year-old stage 53-year-old stage 88-year-old stage 84-year-old stage 82-year-old stage 80-year-old stage 72-year-old stage 81-year-old stage 74-year-old stage Adult stage 90 year-old and over stage 86-year-old stage 70-year-old stage 60-year-old stage 78-year-old stage 63-year-old stage 76-year-old stage 79-year-old stage 73-year-old stage 83-year-old stage

Parkinson disease Normal

Female Male

10x multiome

Nucleus

Homo sapiens

T cell Glutamatergic neuron Oligodendrocyte precursor cell Oligodendrocyte Matrix d1 medium spiny neuron Capillary endothelial cell Cerebellar golgi cell Smooth muscle cell Dopaminergic neuron Pvalb chandelier gabaergic interneuron Lamp5 gabaergic interneuron Ependymal cell Microglial cell Vip gabaergic interneuron Granule cell Molecular layer interneuron Matrix d2 medium spiny neuron Pvalb gabaergic interneuron Bergmann glial cell Pericyte Perivascular macrophage Purkinje cell Astrocyte Fibroblast Sst gabaergic interneuron Gabaergic neuron Medium spiny neuron

Middle temporal gyrus Cingulate gyrus Substantia nigra Cerebellum Putamen

69-year-old stage 75-year-old stage 89-year-old stage 87-year-old stage 71-year-old stage 85-year-old stage 53-year-old stage 88-year-old stage 84-year-old stage 82-year-old stage 80-year-old stage 72-year-old stage 81-year-old stage 74-year-old stage Adult stage 90 year-old and over stage 86-year-old stage 70-year-old stage 60-year-old stage 78-year-old stage 63-year-old stage 76-year-old stage 79-year-old stage 73-year-old stage 83-year-old stage

Parkinson disease Normal

Female Male

10x multiome

Nucleus

Mus musculus

Glutamatergic neuron Oligodendrocyte precursor cell Endothelial cell Hypendymal cell Oligodendrocyte Vascular leptomeningeal cell Cholinergic neuron Smooth muscle cell Tanycyte Dopaminergic neuron Lymphocyte Ependymal cell Macrophage Microglial cell Histaminergic neuron Neuroblast (sensu vertebrata) Olfactory ensheathing cell Glycinergic neuron Choroid plexus epithelial cell Bergmann glial cell Pericyte Monocyte Astrocyte Dendritic cell Gabaergic neuron

Striatum Thalamic complex Neocortex Hindbrain Pallidum Midbrain Cortical subplate White matter Cerebellum Brain Hypothalamus Ventricular system of brain Hippocampal formation

9-week-old stage

Normal

Female

Merfish

Homo sapiens

T cell L2/3 intratelencephalic projecting glutamatergic neuron L5/6 near-projecting glutamatergic neuron Natural killer cell Oligodendrocyte precursor cell Endothelial cell Oligodendrocyte L6b glutamatergic neuron of the primary motor cortex Vascular leptomeningeal cell Smooth muscle cell Lamp5 gabaergic interneuron Microglial cell Vip gabaergic interneuron L2/3-6 intratelencephalic projecting glutamatergic neuron Plasma cell L5 extratelencephalic projecting glutamatergic cortical neuron L6 corticothalamic-projecting glutamatergic cortical neuron Pvalb gabaergic interneuron B cell Pericyte Perivascular macrophage L6 intratelencephalic projecting glutamatergic neuron Astrocyte Sst gabaergic interneuron Gabaergic neuron

Dorsolateral prefrontal cortex

66-year-old stage 69-year-old stage 75-year-old stage 65-year-old stage 42-year-old stage 89-year-old stage 43-year-old stage 87-year-old stage 71-year-old stage 85-year-old stage 53-year-old stage 61-year-old stage 88-year-old stage 52-year-old stage 54-year-old stage 68-year-old stage 48-year-old stage 39-year-old stage 38-year-old stage 56-year-old stage 55-year-old stage 84-year-old stage 82-year-old stage 50-year-old stage 80-year-old stage 28-year-old stage 51-year-old stage 57-year-old stage 72-year-old stage 81-year-old stage 74-year-old stage 80 year-old and over stage 49-year-old stage 24-year-old stage 35-year-old stage 58-year-old stage 59-year-old stage 25-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 86-year-old stage 41-year-old stage 70-year-old stage 46-year-old stage 60-year-old stage 78-year-old stage 31-year-old stage 36-year-old stage 19-year-old stage 63-year-old stage 20-year-old stage 47-year-old stage 76-year-old stage 79-year-old stage 73-year-old stage 83-year-old stage 27-year-old stage 40-year-old stage

Lewy body dementia Parkinson disease Amyotrophic lateral sclerosis Argyrophilic grain disease Brain neoplasm Dementia Alzheimer disease Frontotemporal dementia Normal pressure hydrocephalus Schizophrenia Progressive supranuclear palsy Head injury Major depressive disorder Multiple sclerosis Post-traumatic stress disorder Tauopathy Vascular dementia Normal

Female Male

10x 3' v3

Nucleus

Homo sapiens

Visceromotor neuron Ganglion interneuron Endocardial cell Bipolar neuron Blood vessel endothelial cell Stromal cell Endothelial cell of lymphatic vessel Glutamatergic neuron Chorionic trophoblast cell Oligodendrocyte Chromaffin cell Neuroendocrine cell Retinal ganglion cell Retinal pigment epithelial cell Stellate neuron Corneal epithelial cell Hepatoblast Trophoblast giant cell Enteric neuron Extravillous trophoblast Sympathetic neuron Cortical cell of adrenal gland Schwann cell Taste receptor cell Smooth muscle cell Skeletal muscle satellite cell Inhibitory interneuron Hepatic stellate cell Endothelial cell of vascular tree Goblet cell Thymocyte Photoreceptor cell Tuft cell Endocrine cell Microglial cell Granule cell Neuron associated cell (sensu vertebrata) Innate lymphoid cell Dermis microvascular lymphatic vessel endothelial cell Myeloid cell Ventricular cardiac muscle cell Hematopoietic stem cell Glial cell Intestinal epithelial cell Retina horizontal cell Mesangial cell Megakaryocyte Squamous epithelial cell Amacrine cell Acinar cell Mesothelial cell Cell of skeletal muscle Epithelial cell of lower respiratory tract Ciliated epithelial cell Cardiac muscle cell Macroglial cell Lens fiber cell Professional antigen presenting cell Mueller cell Epicardial adipocyte Neuron Regular atrial cardiac myocyte Purkinje cell Pancreatic ductal cell Syncytiotrophoblast cell Erythroblast Astrocyte Unipolar brush cell Epithelial cell of thymus Gabaergic neuron Hematopoietic cell

Lung Thymus Stomach Liver Telencephalon Kidney Eye Intestine Placenta Heart Muscle organ Cerebellum Pancreas Adrenal gland Spleen

13th week post-fertilization stage 14th week post-fertilization stage 15th week post-fertilization stage 17th week post-fertilization stage 12th week post-fertilization stage 16th week post-fertilization stage 10th week post-fertilization stage 18th week post-fertilization stage

Normal Trisomy 18

Female Male

Sci-rna-seq3

Nucleus Cell

Homo sapiens

Central memory cd4-positive, alpha-beta t cell T cell Club cell Cd1c-positive myeloid dendritic cell Mature conventional dendritic cell Secretory cell Olfactory epithelial cell Globose cell of olfactory epithelium Cd8-positive, alpha-beta t cell Cd141-positive myeloid dendritic cell Ionocyte Plasmacytoid dendritic cell Goblet cell Naive thymus-derived cd8-positive, alpha-beta t cell Tuft cell Macrophage Type i cell of adrenal medulla Deuterosomal cell Respiratory basal cell Plasma cell Cd4-positive, alpha-beta t cell Respiratory tract suprabasal cell Ciliated olfactory receptor neuron Professional antigen presenting cell Naive thymus-derived cd4-positive, alpha-beta t cell Mucus secreting cell Naive b cell Multiciliated epithelial cell Dendritic cell Effector memory cd8-positive, alpha-beta t cell Olfactory epithelial supporting cell

Olfactory epithelium

66-year-old stage 69-year-old stage 37-year-old stage 75-year-old stage 21-year-old stage 65-year-old stage 42-year-old stage 26-year-old stage 87-year-old stage 71-year-old stage 85-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 30-year-old stage 39-year-old stage 44-year-old stage 38-year-old stage 56-year-old stage 55-year-old stage 82-year-old stage 50-year-old stage 90-year-old stage 80-year-old stage 28-year-old stage 51-year-old stage 57-year-old stage 72-year-old stage 81-year-old stage 74-year-old stage 49-year-old stage 24-year-old stage 23-year-old stage 58-year-old stage 59-year-old stage 25-year-old stage Adult stage 67-year-old stage 32-year-old stage 77-year-old stage 33-year-old stage 64-year-old stage 62-year-old stage 86-year-old stage 41-year-old stage 70-year-old stage 46-year-old stage 78-year-old stage 31-year-old stage 36-year-old stage 22-year-old stage 20-year-old stage 47-year-old stage 76-year-old stage 79-year-old stage 73-year-old stage 83-year-old stage 27-year-old stage

Alzheimer disease Parkinson disease Normal

Female Male

Cell

Homo sapiens

Neutrophil Germinal center b cell Cd1c-positive myeloid dendritic cell Igm plasma cell Mature conventional dendritic cell Intestinal crypt stem cell of colon Natural killer cell Endothelial cell of lymphatic vessel Gamma-delta t cell Reticular cell Best4+ enterocyte Mature nk t cell Mast cell Cd8-positive, alpha-beta t cell Platelet Iga plasma cell Endothelial cell of artery Schwann cell Classical monocyte Plasmacytoid dendritic cell Igg plasma cell Naive thymus-derived cd8-positive, alpha-beta t cell Transit amplifying cell of colon Macrophage Tuft cell of colon Memory b cell Innate lymphoid cell Regulatory t cell Mature b cell Plasmablast Cd4-positive, alpha-beta t cell Vein endothelial cell Eosinophil Malignant cell Colon goblet cell Pericyte Granulocyte monocyte progenitor cell Naive thymus-derived cd4-positive, alpha-beta t cell Naive b cell Fibroblast Colonocyte Non-classical monocyte Enteroendocrine cell of colon

Ascending colon Colonic epithelium Rectosigmoid junction Colorectum Caecum Liver Right colon Colon Hepatic flexure of colon Mucosa of transverse colon Left colon Rectum Splenic flexure of colon Transverse colon Caecum epithelium Blood Lymph node Colorectal mucosa Descending colon Sigmoid colon Mesenteric lymph node Hepatic cecum

66-year-old stage 69-year-old stage 37-year-old stage 75-year-old stage 91-year-old stage 34-year-old stage 65-year-old stage 42-year-old stage 26-year-old stage 89-year-old stage 43-year-old stage Sixth decade stage 71-year-old stage 85-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 30-year-old stage 44-year-old stage 29-year-old stage 38-year-old stage 56-year-old stage Fifth decade stage 55-year-old stage 84-year-old stage 82-year-old stage 50-year-old stage 90-year-old stage 80-year-old stage 51-year-old stage 57-year-old stage 72-year-old stage Third decade stage 81-year-old stage 74-year-old stage 49-year-old stage 35-year-old stage Seventh decade stage 58-year-old stage 59-year-old stage Adult stage 67-year-old stage 77-year-old stage 33-year-old stage 64-year-old stage 45-year-old stage 62-year-old stage 86-year-old stage 41-year-old stage 70-year-old stage 46-year-old stage 60-year-old stage 78-year-old stage 31-year-old stage 36-year-old stage Fourth decade stage 63-year-old stage Eighth decade stage 47-year-old stage 76-year-old stage 79-year-old stage 73-year-old stage 83-year-old stage Ninth decade stage 40-year-old stage

Colon adenocarcinoma Mucinous adenocarcinoma Colon adenoma Colorectal tubulovillous adenoma Tubular adenoma Colon carcinoma Colon sessile serrated adenoma/polyp Colorectal adenocarcinoma Colorectal cancer Colorectal neoplasm Hyperplastic polyp Metastasis from malignant tumor of colon Normal Polyp of colon Rectum adenocarcinoma

Female Male

10x 3' v1 10x 3' v2 10x 3' v3 10x 5' transcription profiling 10x 5' v1 10x 5' v2 Bd rhapsody whole transcriptome analysis Fluidigm c1-based library preparation Gexscope technology Smart-seq2 Trudrop

Cell

Homo sapiens

Central memory cd4-positive, alpha-beta t cell T cell Cd1c-positive myeloid dendritic cell Mature gamma-delta t cell Natural killer cell Erythrocyte Platelet Cd141-positive myeloid dendritic cell Effector memory cd4-positive, alpha-beta t cell Cd8aa(i) thymocyte Plasmacytoid dendritic cell Basophil mast progenitor cell Cd8-positive, alpha-beta memory t cell Be cell Memory regulatory t cell Naive thymus-derived cd8-positive, alpha-beta t cell Memory b cell Axl+ dendritic cell, human Cd16-positive, cd56-dim natural killer cell, human Innate lymphoid cell Common myeloid progenitor Plasma cell Naive regulatory t cell Memory ccr4-positive regulatory t cell Cd14-low, cd16-positive monocyte Cd4-positive, alpha-beta memory t cell Naive thymus-derived cd4-positive, alpha-beta t cell Common lymphoid progenitor Mucosal invariant t cell Cd8-positive, alpha-beta regulatory t cell Transitional stage b cell Cd14-positive, cd16-negative classical monocyte Central memory cd8-positive, alpha-beta t cell Naive b cell Double negative thymocyte Cd16-negative, cd56-bright natural killer cell, human Effector memory cd8-positive, alpha-beta t cell

Blood

66-year-old stage 69-year-old stage 75-year-old stage 65-year-old stage 42-year-old stage 89-year-old stage 43-year-old stage 87-year-old stage 71-year-old stage 85-year-old stage 53-year-old stage 61-year-old stage 88-year-old stage 52-year-old stage 54-year-old stage 68-year-old stage 48-year-old stage 44-year-old stage 56-year-old stage 55-year-old stage 84-year-old stage 82-year-old stage 50-year-old stage 80-year-old stage 51-year-old stage 57-year-old stage 72-year-old stage 81-year-old stage 74-year-old stage 80 year-old and over stage 49-year-old stage 58-year-old stage 59-year-old stage 67-year-old stage 77-year-old stage 64-year-old stage 45-year-old stage 62-year-old stage 86-year-old stage 41-year-old stage 70-year-old stage 46-year-old stage 60-year-old stage 78-year-old stage 63-year-old stage 47-year-old stage 76-year-old stage 79-year-old stage 73-year-old stage 83-year-old stage 40-year-old stage

Cytomegalovirus infection Normal

Female Male

10x gene expression flex

Cell

Mus musculus

Osteoblast Mesodermal cell Lateral mesodermal cell Fibroblast Chondrocyte

Embryo

Theiler stage 22 Theiler stage 27 Theiler stage 24 Theiler stage 18 Theiler stage 25 Theiler stage 14 Theiler stage 16 Theiler stage 17 Theiler stage 15 Theiler stage 19 Theiler stage 26 Theiler stage 13 Theiler stage 20 Theiler stage 12 Theiler stage 21 Theiler stage 23

Normal

Female Male

Sci-rna-seq3

Nucleus

Homo sapiens

Diffuse bipolar 1 cell Diffuse bipolar 4 cell Gabaergic amacrine cell Off midget ganglion cell Diffuse bipolar 2 cell Retinal ganglion cell Retinal pigment epithelial cell Off parasol ganglion cell Offx cell On midget ganglion cell Rod bipolar cell S cone cell On parasol ganglion cell Invaginating midget bipolar cell Retinal bipolar neuron H2 horizontal cell Microglial cell Retinal cone cell Glycinergic amacrine cell Retinal rod cell Flat midget bipolar cell Amacrine cell Diffuse bipolar 3a cell Starburst amacrine cell On-blue cone bipolar cell Diffuse bipolar 6 cell Mueller cell Giant bipolar cell Astrocyte H1 horizontal cell Diffuse bipolar 3b cell

Peripheral region of retina Macula lutea proper Fovea centralis Macula lutea

66-year-old stage 69-year-old stage 75-year-old stage 21-year-old stage 34-year-old stage 65-year-old stage 43-year-old stage 71-year-old stage 85-year-old stage 53-year-old stage 88-year-old stage 52-year-old stage 68-year-old stage 30-year-old stage 17-year-old stage 84-year-old stage 15-year-old stage 82-year-old stage 50-year-old stage 80-year-old stage 72-year-old stage 81-year-old stage 74-year-old stage 80 year-old and over stage 24-year-old stage 16-year-old stage 58-year-old stage 25-year-old stage 67-year-old stage Late adult stage 90 year-old and over stage 3-year-old stage 32-year-old stage 77-year-old stage 64-year-old stage 62-year-old stage 86-year-old stage 41-year-old stage 70-year-old stage 46-year-old stage 60-year-old stage 78-year-old stage 18-year-old stage 60-79 year-old stage 63-year-old stage Eighth decade stage 47-year-old stage 76-year-old stage 73-year-old stage 83-year-old stage Prime adult stage 11-year-old stage 27-year-old stage 10-year-old stage

Normal

Female Male

10x 3' v3

Nucleus

Homo sapiens

Diffuse bipolar 1 cell Diffuse bipolar 4 cell Gabaergic amacrine cell Off midget ganglion cell Diffuse bipolar 2 cell Retinal ganglion cell Retinal pigment epithelial cell Off parasol ganglion cell Offx cell On midget ganglion cell Rod bipolar cell S cone cell On parasol ganglion cell Invaginating midget bipolar cell Retinal bipolar neuron H2 horizontal cell Microglial cell Retinal cone cell Glycinergic amacrine cell Retinal rod cell Flat midget bipolar cell Amacrine cell Diffuse bipolar 3a cell Starburst amacrine cell On-blue cone bipolar cell Diffuse bipolar 6 cell Mueller cell Giant bipolar cell Astrocyte H1 horizontal cell Diffuse bipolar 3b cell

Normal

10x 3' v3