Mus musculus

Hypothalamus cell Retinal pigment epithelial cell Neural cell Ependymal cell Retinal progenitor cell Astrocyte

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

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 Intermediate monocyte 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

37-year-old stage 34-year-old stage 30-year-old stage 29-year-old stage 28-year-old stage 35-year-old stage 32-year-old stage 33-year-old stage 31-year-old stage 36-year-old stage

Normal

Male

10x 3' v3

Cell

Homo sapiens

Glioblast Cell Erythrocyte Oligodendrocyte Neuroblast (sensu nematoda and protostomia) Neuroplacodal cell Neural crest cell Macrophage Neuroblast (sensu vertebrata) Radial glial cell Neuron Fibroblast

Choroid plexus epithelium Striatum Medulla oblongata Hindbrain Telencephalon Cortex Midbrain Dorsal plus ventral thalamus Lower layers of the cortex Frontal cortex Entorhinal cortex Midbrain tectum Metencephalon Basal forebrain Cerebellum Brain Hypothalamus Cerebellar peduncular complex Upper layers of the cortex Caudate-putamen Hippocampal formation Diencephalon Pons Cerebral subcortex Occipital cortex Forebrain Head

13th week post-fertilization stage 14th week post-fertilization stage 15th week post-fertilization stage 12th week post-fertilization stage Carnegie stage 20 9th week post-fertilization stage 10th week post-fertilization stage Carnegie stage 22 Carnegie stage 16 Carnegie stage 15 Carnegie stage 18 11th week post-fertilization stage

Normal

10x 3' v3 10x 3' v2

Cell

Homo sapiens

Angiogenic pericyte Germinal center b cell Muscle cell Cycling t cell Dendritic cell, human Igm plasma cell Intestine goblet cell Endothelial cell of lymphatic vessel Erythrocyte Follicular dendritic cell Gamma-delta t cell Best4+ enterocyte Endothelial cell Afferent neuron Pro-b cell Interstitial cell of cajal Type g enteroendocrine cell Mast cell Iga plasma cell Enteric neuron Immature pericyte Basal cell Endothelial cell of artery Capillary endothelial cell Melanocyte Ionocyte Smooth muscle cell Paneth cell Enteroglial cell Plasmacytoid dendritic cell, human Epithelial cell Inhibitory motor neuron Peptic cell Igg plasma cell Fibroblast of gingiva Precursor b cell Enteroendocrine cell Glandular cell of esophagus Mesodermal cell Cd8-positive, alpha-beta memory t cell Myoepithelial cell Group 3 innate lymphoid cell Naive thymus-derived cd8-positive, alpha-beta t cell T-helper 17 cell Macrophage Intestinal crypt stem cell Memory b cell Cd16-positive, cd56-dim natural killer cell, human Regulatory t cell Neuroblast (sensu vertebrata) Type ec enteroendocrine cell Fibroblastic reticular cell Plasmablast Parietal cell Tuft cell of small intestine Keratinocyte Trem2-positive macrophage Acinar cell of salivary gland Enterocyte Salivary gland glandular cell Vein endothelial cell Mesenchymal cell Gastrointestinal tract (lamina propria) macrophage Motor neuron Neutrophil progenitor cell Eosinophil Megakaryocyte Langerhans cell Interneuron Transit amplifying cell T follicular helper cell Cd4-positive, alpha-beta memory t cell Mesothelial cell Pericyte Mucous neck cell of gastric gland Progenitor cell Type x enteroendocrine cell Foveolar cell of stomach Naive thymus-derived cd4-positive, alpha-beta t cell Mucosal invariant t cell Monocyte Cycling basal cell Vascular associated smooth muscle cell Naive b cell Myofibroblast cell Conventional dendritic cell Fibroblast Colonocyte Cd16-negative, cd56-bright natural killer cell, human M cell of gut Effector memory cd8-positive, alpha-beta t cell

Ascending colon Colonic mucosa Stomach Duodenum Colonic epithelium Ileal epithelium Rectosigmoid junction Pyloric antrum Caecum Small intestine Gingiva Ileum Ileum lamina propria Lamina propria of mucosa of colon Colon Epithelium of rectum Lamina propria of small intestine Epithelium of esophagus Intestine Buccal mucosa Body of stomach Mucosa of transverse colon Vermiform appendix Cecum mucosa Epithelium of small intestine Pylorus Rectum Esophagus Jejunum Duodenal epithelium Transverse colon Periodontium Caecum epithelium Parotid gland Mucosa of sigmoid colon Descending colon Sigmoid colon Labial gland Epithelium of stomach Mesenteric lymph node

66-year-old stage 69-year-old stage Carnegie stage 19 37-year-old stage 75-year-old stage Pediatric stage 19th week post-fertilization stage 21-year-old stage 13-year-old stage 21st week post-fertilization stage 34-year-old stage 65-year-old stage 26-year-old stage 43-year-old stage Sixth decade stage 87-year-old stage 13th week post-fertilization stage 85-year-old stage 61-year-old stage 2-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 29-year-old stage 56-year-old stage Fifth decade stage 55-year-old stage 84-year-old stage 15th week post-fertilization stage 50-year-old stage 80-year-old stage 28-year-old stage 51-year-old stage 17th week post-fertilization stage 57-year-old stage 12-year-old stage 72-year-old stage 12th week post-fertilization stage Third decade stage 16th week post-fertilization stage 81-year-old stage 9th week post-fertilization stage 74-year-old stage 9-year-old stage 10th week post-fertilization stage 14-year-old stage 24-year-old stage 23-year-old stage 35-year-old stage Seventh decade stage 58-year-old stage Embryonic stage 59-year-old stage 25-year-old stage Adult stage 67-year-old stage 18th week post-fertilization stage Carnegie stage 17 2-month-old stage 32-year-old stage 77-year-old stage 33-year-old stage Carnegie stage 22 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 18-year-old stage 31-year-old stage 36-year-old stage Fourth decade stage 22-year-old stage Newborn stage (0-28 days) 63-year-old stage 20-year-old stage Carnegie stage 16 Eighth decade stage 76-year-old stage Prime adult stage 5-year-old stage 11-year-old stage 6-year-old stage Young adult stage 10-year-old stage Carnegie stage 18 4-year-old stage 11th week post-fertilization stage Juvenile stage (5-14 yo)

Crohn disease Celiac disease Colorectal cancer Gastric cancer Inflammatory bowel disease Normal Ulcerative colitis

Female Male

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

Cell

Mus musculus

Cell

Normal

Dronc-seq Merfish 10x 3' v2

Macaca mulatta

Cerebellar neuron Glutamatergic neuron Oligodendrocyte precursor cell Serotonergic neuron Oligodendrocyte Basket cell Dopaminergic neuron Brain vascular cell Ependymal cell Microglial cell Neuron Astrocyte Gabaergic neuron Medium spiny neuron

Dorsolateral prefrontal cortex Brodmann (1909) area 19 Medial dorsal nucleus of thalamus Primary visual cortex Ventral lateral nucleus of thalamus Inferior temporal gyrus Medulla oblongata Prefrontal cortex Midbrain Entorhinal cortex Nucleus accumbens Cerebrocerebellum Primary somatosensory cortex Primary auditory cortex Primary motor cortex Inferior parietal cortex Head of caudate nucleus Corpus callosum Hippocampal formation Perirhinal cortex Pons Cerebellar vermis Anterior cingulate cortex Superior temporal sulcus Superior parietal cortex Lateral geniculate body Amygdala

Juvenile stage Prime adult stage

Normal

Female Male

Sci-rna-seq3

Nucleus

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 37-year-old stage 75-year-old stage 21-year-old stage 13-year-old stage 34-year-old stage 65-year-old stage 42-year-old stage 26-year-old stage 43-year-old stage 71-year-old stage 85-year-old stage 53-year-old stage 61-year-old stage 2-year-old stage 52-year-old stage 54-year-old stage 68-year-old stage 3-month-old stage 48-year-old stage 30-year-old stage 39-year-old stage 44-year-old stage 17-year-old stage 29-year-old stage 38-year-old stage 56-year-old stage 8-year-old stage 55-year-old stage 84-year-old stage 15-year-old stage 50-year-old stage 28-year-old stage 51-year-old stage 57-year-old stage 12-year-old stage 74-year-old stage 6-month-old stage 49-year-old stage 14-year-old stage 24-year-old stage 16-year-old stage 23-year-old stage 35-year-old stage 58-year-old stage 59-year-old stage 25-year-old stage 67-year-old stage 2-month-old stage 3-year-old stage 32-year-old stage 33-year-old stage 45-year-old stage 62-year-old stage 41-year-old stage 46-year-old stage 60-year-old stage 78-year-old stage 18-year-old stage 31-year-old stage 36-year-old stage 1-month-old stage 22-year-old stage 19-year-old stage 63-year-old stage 20-year-old stage 47-year-old stage 4-month-old stage 76-year-old stage 79-year-old stage 73-year-old stage 83-year-old stage 5-year-old stage 27-year-old stage 6-year-old stage 40-year-old stage 10-year-old stage 4-year-old stage

Atherosclerosis Tardive dyskinesia Schizoaffective bipolar disorder Bipolar i disorder Anorexia nervosa Obsessive-compulsive disorder Attention deficit-hyperactivity disorder Brain neoplasm Bulimia nervosa Post-traumatic stress disorder Type 1 diabetes mellitus Type 2 diabetes mellitus Bipolar ii disorder Bipolar disorder Diabetes mellitus Schizophrenia Epilepsy Major depressive disorder Normal Schizoaffective depressive disorder

Female Male

10x 3' v3

Nucleus

Homo sapiens

Neutrophil Mature gamma-delta t cell Cd14-positive, cd16-positive monocyte Ciliated cell Natural killer cell Mature alpha-beta t cell Secretory cell Mast cell Cd8-positive, alpha-beta t cell Epithelial cell Macrophage Plasma cell Megakaryocyte Squamous epithelial cell B cell Monocyte Cd14-positive, cd16-negative classical monocyte Dendritic cell

Lung Saliva Blood

66-year-old stage 69-year-old stage 37-year-old stage 34-year-old stage 65-year-old stage 42-year-old stage 26-year-old stage 43-year-old stage 87-year-old stage 71-year-old stage 53-year-old stage 61-year-old stage 52-year-old stage 54-year-old stage 48-year-old stage 30-year-old stage 39-year-old stage 44-year-old stage 29-year-old stage 38-year-old stage 56-year-old stage 8-year-old stage 55-year-old stage 92-year-old stage 15-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 49-year-old stage 16-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 33-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 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 6-year-old stage 40-year-old stage

Covid-19 Normal

Female Male

10x 5' v2 10x 3' v3

Cell

Homo sapiens

Homo sapiens

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

Dorsolateral prefrontal cortex

69-year-old stage 75-year-old stage 42-year-old stage 89-year-old stage 87-year-old stage 85-year-old stage 88-year-old stage 68-year-old stage 29-year-old stage 84-year-old stage 82-year-old stage 50-year-old stage 80-year-old stage 72-year-old stage 81-year-old stage 80 year-old and over stage 77-year-old stage 86-year-old stage 70-year-old stage 78-year-old stage 83-year-old stage

Dementia Normal

Female Male

10x multiome 10x 3' v3

Nucleus

Homo sapiens

Neutrophil Podocyte Cycling t cell Migratory dendritic cell Endothelial cell of venule Natural killer cell Kidney collecting duct beta-intercalated cell Parietal epithelial cell Erythrocyte Renal interstitial pericyte Endothelial cell Kidney loop of henle thin descending limb epithelial cell Cd8-alpha-positive thymic conventional dendritic cell Kidney interstitial fibroblast Mast cell Kidney loop of henle cortical thick ascending limb epithelial cell Kidney resident macrophage Peritubular capillary endothelial cell Kidney collecting duct intercalated cell Kidney interstitial myofibroblast Renal medullary fibroblast Classical monocyte Epithelial cell of proximal tubule Plasmacytoid dendritic cell, human Neural cell Epithelial cell of proximal tubule segment 1 Vasa recta descending limb cell Adipocyte Group 3 innate lymphoid cell Cycling macrophage Macrophage Effector memory cd8-positive, alpha-beta t cell, terminally differentiated Kidney distal convoluted tubule epithelial cell Kidney collecting duct principal cell Kidney connecting tubule epithelial cell Kidney connecting tubule principal cell Kidney outer medulla peritubular capillary cell Kidney loop of henle thick ascending limb epithelial cell Vasa recta ascending limb cell Vasa recta cell Epithelial cell of proximal tubule segment 3 Macula densa epithelial cell Plasma cell Kidney cortex collecting duct principal cell Vein endothelial cell Juxtaglomerular complex cell Mesangial cell Naive regulatory t cell Epithelial cell of proximal tubule segment 2 Kidney collecting duct alpha-intercalated cell Cd8-alpha-negative thymic conventional dendritic cell B cell Naive thymus-derived cd4-positive, alpha-beta t cell Mucosal invariant t cell Vascular associated smooth muscle cell Kidney loop of henle thin ascending limb epithelial cell Glomerular capillary endothelial cell Papillary tips cell Adventitial fibroblast Effector memory cd8-positive, alpha-beta t cell Kidney efferent arteriole endothelial cell Non-classical monocyte Kidney cortex peritubular capillary cell

Renal medulla Renal papilla Kidney Cortex of kidney

66-year-old stage 69-year-old stage 43-year-old stage Sixth decade stage 54-year-old stage 29-year-old stage 56-year-old stage Fifth decade stage 57-year-old stage Third decade stage 49-year-old stage 14-year-old stage Seventh decade stage 59-year-old stage 64-year-old stage 45-year-old stage 70-year-old stage 36-year-old stage Fourth decade stage 63-year-old stage Eighth decade stage 76-year-old stage Tenth decade stage Ninth decade stage

Acute kidney failure Chronic kidney disease Normal

Female Male

10x multiome 10x 3' v3

Nucleus

Homo sapiens

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

Middle temporal gyrus

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 85-year-old stage 88-year-old stage 68-year-old stage 29-year-old stage 84-year-old stage 82-year-old stage 50-year-old stage 80-year-old stage 72-year-old stage 81-year-old stage 80 year-old and over stage 77-year-old stage 86-year-old stage 70-year-old stage 60-year-old stage 78-year-old stage 83-year-old stage

Dementia Normal

Female Male

10x multiome 10x 3' v3

Nucleus