Mus musculus

Retinal bipolar neuron Retinal cone cell Gabaergic amacrine cell Type 5 cone bipolar cell (sensu mus) Pericyte Amacrine cell Type 9 cone bipolar cell (sensu mus) Rod bipolar cell Mueller cell Retinal ganglion cell Retinal pigment epithelial cell Type 1 cone bipolar cell (sensu mus) Type 6 cone bipolar cell (sensu mus) Type 4 cone bipolar cell (sensu mus) Type 2 cone bipolar cell (sensu mus) Type 7 cone bipolar cell (sensu mus) Type 3a cone bipolar cell Microglial cell Type 8 cone bipolar cell (sensu mus) Type 5a cone bipolar cell Endothelial cell Retinal rod cell Type 5b cone bipolar cell Glycinergic amacrine cell Astrocyte Type 3b cone bipolar cell Retina horizontal cell

Normal

10x 3' v2 10x 3' v3 Drop-seq

Mus musculus

Retinal bipolar neuron Retinal cone cell Gabaergic amacrine cell Type 5 cone bipolar cell (sensu mus) Pericyte Amacrine cell Type 9 cone bipolar cell (sensu mus) Rod bipolar cell Mueller cell Retinal ganglion cell Retinal pigment epithelial cell Type 1 cone bipolar cell (sensu mus) Type 6 cone bipolar cell (sensu mus) Type 4 cone bipolar cell (sensu mus) Type 2 cone bipolar cell (sensu mus) Type 7 cone bipolar cell (sensu mus) Type 3a cone bipolar cell Microglial cell Type 8 cone bipolar cell (sensu mus) Type 5a cone bipolar cell Endothelial cell Retinal rod cell Type 5b cone bipolar cell Glycinergic amacrine cell Astrocyte Type 3b cone bipolar cell Retina horizontal cell

Optic cup Retina

25-week-old stage Prime adult stage 12-week-old stage Postnatal stage 8-week-old stage 9-week-old stage 4-month-old stage 2-week-old stage 7-week-old stage 11-week-old stage 5-week-old stage

Normal

Male

10x 3' v2 10x 3' v3 Drop-seq

Cell

Homo sapiens

L2/3-6 intratelencephalic projecting glutamatergic neuron

Middle temporal gyrus

80 year-old and over stage 85-year-old stage 80-year-old stage 50-year-old stage 65-year-old stage 68-year-old stage 82-year-old stage 43-year-old stage 29-year-old stage Adult stage 75-year-old stage 84-year-old stage 86-year-old stage 83-year-old stage 89-year-old stage 77-year-old stage 78-year-old stage 70-year-old stage 81-year-old stage 69-year-old stage 88-year-old stage 87-year-old stage 60-year-old stage 72-year-old stage

Normal Dementia

Female Male

10x 3' v3 10x multiome

Nucleus

Homo sapiens

Megakaryocyte Dendritic cell, human Non-classical monocyte Naive b cell Classical monocyte Regulatory t cell Cd8-positive, alpha-beta memory t cell, cd45ro-positive Mast cell Progenitor cell Alpha-beta t cell Group 3 innate lymphoid cell Naive thymus-derived cd8-positive, alpha-beta t cell Memory b cell Precursor b cell Naive thymus-derived cd4-positive, alpha-beta t cell Macrophage Gamma-delta t cell Cd8-positive, alpha-beta memory t cell Plasmablast Cd16-negative, cd56-bright natural killer cell, human Cd4-positive helper t cell Erythroid lineage cell Lymphocyte Pro-b cell Conventional dendritic cell Germinal center b cell Plasma cell Effector memory cd4-positive, alpha-beta t cell Alveolar macrophage Mucosal invariant t cell Plasmacytoid dendritic cell Effector memory cd8-positive, alpha-beta t cell, terminally differentiated Cd16-positive, cd56-dim natural killer cell, human T follicular helper cell

Liver Thoracic lymph node Bone marrow Ileum Jejunum lamina propria Sigmoid colon Duodenum Spleen Omentum Jejunal epithelium Blood Mesenteric lymph node Caecum Thymus Transverse colon Lung Skeletal muscle tissue

Eighth decade stage 56-year-old stage Seventh decade stage 67-year-old stage Sixth decade stage

Normal

Female Male

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

Cell

Homo sapiens

Erythrocyte Mast cell Myeloid cell Epithelial cell Hepatocyte Lymphocyte Stromal cell Plasmacytoid dendritic cell Endothelial cell B cell

Normal Primary biliary cholangitis Hepatocellular carcinoma Metabolic dysfunction-associated steatohepatitis Alcoholic liver cirrhosis

10x 3' v2 10x 3' v3

Homo sapiens

Cd14-positive, cd16-negative classical monocyte Cd14-low, cd16-positive monocyte Intermediate monocyte

Blood

64-year-old stage 26-year-old stage 65-year-old stage 35-year-old stage 63-year-old stage 29-year-old stage 58-year-old stage 34-year-old stage 31-year-old stage 59-year-old stage 25-year-old stage 12-year-old stage 61-year-old stage 57-year-old stage 11-year-old stage 56-year-old stage 55-year-old stage 36-year-old stage 32-year-old stage 60-year-old stage 62-year-old stage 28-year-old stage 30-year-old stage 27-year-old stage 33-year-old stage

Normal Cytomegalovirus infection

Female Male

10x 3' v3

Cell

Homo sapiens

Syncytiotrophoblast cell Natural killer cell Endothelial cell of lymphatic vessel Regulatory t cell Decidual natural killer cell, human Uterine smooth muscle cell Extravillous trophoblast Macrophage Placental villous trophoblast Dendritic cell T cell Granulocyte Epithelial cell Endothelial cell of placenta Plasma cell Trophoblast giant cell Group 3 innate lymphoid cell, human Stromal cell Hofbauer cell Endothelial cell of uterus B cell Embryonic fibroblast

Placenta Blood Decidua basalis Decidua

11th week post-fertilization stage Carnegie stage 18 9th week post-fertilization stage Carnegie stage 14 Carnegie stage 23 Carnegie stage 22 12th week post-fertilization stage 10th week post-fertilization stage Carnegie stage 16

Normal

Female

10x 3' v2 10x 3' v3 10x multiome

Cell Nucleus

Homo sapiens

Cell of skeletal muscle Interstitial cell of cajal Vascular associated smooth muscle cell Fibroblast Epithelial cell of nephron Enteroendocrine cell Mesothelial cell Osteoblast Glial cell Skeletal muscle satellite cell Epithelial cell Hepatocyte Eurydendroid cell Stromal cell Myofibroblast cell Neuron Endothelial cell Chondrocyte Smooth muscle cell Keratinocyte Melanocyte

Liver Kidney Bone marrow Yolk sac Spleen Skin of body Mesenteric lymph node Gut wall Thymus

15th week post-fertilization stage 11th week post-fertilization stage 14th week post-fertilization stage 9th week post-fertilization stage 13th week post-fertilization stage Carnegie stage 23 Carnegie stage 22 12th week post-fertilization stage 10th week post-fertilization stage 17th week post-fertilization stage 16th week post-fertilization stage Carnegie stage 19 Carnegie stage 20 Carnegie stage 13

Normal

Female Male

10x 3' v2 10x 5' v1

Cell

Homo sapiens

Dendritic cell, human Non-classical monocyte Natural killer cell Erythrocyte Naive b cell Alveolar type 1 fibroblast cell Classical monocyte Endothelial cell of lymphatic vessel Pulmonary alveolar type 1 cell Regulatory t cell Capillary endothelial cell Mast cell Smooth muscle cell of the pulmonary artery Fibroblast Pericyte Club cell Alveolar capillary type 2 endothelial cell Memory b cell Macrophage T cell Mesothelial cell Central memory cd4-positive, alpha-beta t cell Plasmablast Vein endothelial cell Cd16-negative, cd56-bright natural killer cell, human Conventional dendritic cell Pulmonary alveolar type 2 cell Plasma cell Effector memory cd4-positive, alpha-beta t cell Ionocyte Alveolar macrophage Goblet cell Myofibroblast cell Muscle cell Plasmacytoid dendritic cell Lung multiciliated epithelial cell Effector memory cd8-positive, alpha-beta t cell, terminally differentiated Fibroblast of lung Cd16-positive, cd56-dim natural killer cell, human T follicular helper cell Effector memory cd8-positive, alpha-beta t cell Endothelial cell of artery Basal cell

Bronchus Upper lobe of left lung Lung Lower lobe of left lung Lung parenchyma

64-year-old stage 50-year-old stage 65-year-old stage 41-year-old stage 35-year-old stage Fifth decade stage 37-year-old stage 29-year-old stage 58-year-old stage 22-year-old stage 75-year-old stage 31-year-old stage 49-year-old stage 59-year-old stage 54-year-old stage 25-year-old stage 66-year-old stage 61-year-old stage Eighth decade stage 21-year-old stage 46-year-old stage 56-year-old stage Seventh decade stage 20-year-old stage 32-year-old stage 67-year-old stage 62-year-old stage Sixth decade stage 23-year-old stage 51-year-old stage

Normal

Female Male

10x 3' v2 10x 5' transcription profiling

Cell

Mus musculus

Inflammatory macrophage Natural killer cell Schwann cell Classical monocyte Kidney loop of henle cortical thick ascending limb epithelial cell Juxtaglomerular complex cell Kidney interstitial fibroblast Kidney cortex collecting duct principal cell Vascular associated smooth muscle cell Fibroblast Epithelial cell of proximal tubule segment 2 Peritubular capillary endothelial cell Mesangial cell Kidney loop of henle thin ascending limb epithelial cell Renal medullary fibroblast Kidney resident macrophage Epithelial cell of proximal tubule Papillary tips cell Renal cortical fibroblast Kidney collecting duct principal cell Kidney loop of henle medullary thick ascending limb epithelial cell Macrophage Vasa recta descending limb cell Dendritic cell Epithelial cell of proximal tubule segment 1 T cell Kidney loop of henle thick ascending limb epithelial cell Endothelial cell of venule Adventitial fibroblast Vein endothelial cell Kidney cortex peritubular capillary cell Epithelial cell of proximal tubule segment 3 Kidney loop of henle short descending thin limb epithelial cell Parietal epithelial cell Kidney distal convoluted tubule epithelial cell Adipocyte Kidney inner medulla collecting duct epithelial cell Renal beta-intercalated cell Plasma cell Kidney connecting tubule epithelial cell Myofibroblast cell Endothelial cell Vasa recta ascending limb cell Kidney loop of henle thin descending limb epithelial cell B cell Kidney collecting duct alpha-intercalated cell Podocyte Macula densa epithelial cell Glomerular capillary endothelial cell Kidney efferent arteriole endothelial cell

Kidney

7-month-old stage 4-month-old stage 3-month-old stage 20-month-old stage 3-6 month-old mature stage 12-month-old stage 2-month-old stage

Normal Acute kidney failure

Female Male

10x 3' v2 10x multiome

Nucleus

Drosophila melanogaster

Adult renal stem cell Adult brain cell body glial cell Proximal medullary amacrine neuron pm4 Adult malpighian tubule stellate cell of main segment Columnar neuron t1 Adult enteroendocrine cell Enteroblast Transmedullary y neuron tmy14 Transmedullary neuron tm2 Neuron of aristal sensillum Lamina monopolar neuron l5 Adult neuron Transmedullary neuron tm20 Adult antennal olfactory receptor neuron Distal medullary amacrine neuron dm11 Transmedullary y neuron tmy4 Dopaminergic neuron Lamina monopolar neuron l2 Distal medullary amacrine neuron dm10 Transmedullary neuron tm5c Tendon cell Outer photoreceptor cell Adult malpighian tubule bar-shaped cell of initial segment Gustatory receptor neuron Perineurial glial cell Dorsal margin photoreceptor cell Enteroendocrine cell Ensheathing glial cell Gamma kenyon cell Medulla intrinsic neuron mi9 Spermatocyte Johnston organ neuron Adult glial cell Adult olfactory receptor neuron or13a Male accessory gland secondary cell Visceral muscle cell Antennal olfactory receptor neuron of coeloconic sensillum Polar follicle cell Adult olfactory receptor neuron gr21a/63a Early elongation stage spermatid Transmedullary neuron tm9 Labral sense organ mechanosensory neuron T3 neuron Adult brain perineurial glial cell Germline cell Adult midgut enterocyte Nociceptive neuron Transmedullary y neuron tmy8 Leg taste bristle chemosensory neuron Medulla intrinsic neuron mi1 Adult olfactory receptor neuron or65 Lamina monopolar neuron l1 Crystal cell Enterocyte of posterior adult midgut epithelium Photoreceptor cell r7 Adult malpighian tubule principal cell of lower ureter Lobula columnar neuron lc17 Lobula columnar neuron lc10 Dorsal appendage forming follicle cell Early-mid elongation-stage spermatid Fat body cell T2 neuron Stretch follicle cell Head cyst cell Optic-lobe-associated cortex glial cell Adult malpighian tubule principal cell of initial segment Multidendritic neuron Lamina wide-field 2 neuron Transmedullary neuron tm1 Adult enterocyte Distal medullary amacrine neuron dm12 Sensory neuron Medulla intrinsic neuron mi15 Lamina monopolar neuron l3 Chordotonal neuron Olfactory receptor neuron Transmedullary neuron tm4 Proximal medullary amacrine neuron pm2 Adult oenocyte Antennal lobe projection neuron Mechanosensory neuron of leg chordotonal organ Escort cell Eye photoreceptor cell Adult malpighian tubule principal cell Epithelial cell Adult differentiating enterocyte Spermatid Distal medullary amacrine neuron dm8a Distal medullary amacrine neuron dm3 Mid-late elongation-stage spermatid Posterior terminal follicle cell Gustatory receptor neuron of the labellum Adult optic chiasma glial cell Main body follicle cell Leg muscle motor neuron Alpha'/beta' kenyon cell Follicle cell of egg chamber Cardial cell Intestinal stem cell Midgut large flat cell Auditory sensory neuron Maxillary palp olfactory receptor neuron Cell body glial cell Somatic muscle cell Adult olfactory receptor neuron or88a Cns surface glial cell Interfollicle cell Subperineurial glial cell Male accessory gland main cell Indirect flight muscle cell Adult cholinergic neuron Tormogen cell Neuron Transmedullary y neuron tmy5a Muscle cell Kenyon cell Distal medullary amacrine neuron dm9 Centrifugal neuron c3 Adult malpighian tubule principal cell of lower segment Visual pigment cell (sensu nematoda and protostomia) Adult tracheocyte Adult olfactory receptor neuron or92a Transmedullary neuron tm29 Transmedullary neuron tm3 Adult olfactory receptor neuron ir75d Adult abdominal pericardial cell Centrifugal neuron c2 Lamina wide-field 1 neuron Adult astrocyte-like glial cell Eo sensory organ accessory cell Ocellar retinula cell Antennal olfactory receptor neuron of basiconic sensillum Cyst progenitor cell Medulla intrinsic neuron mi4 Ovarian sheath cell Adult olfactory receptor neuron or67d Lobula columnar neuron lc12 Hemocyte (sensu arthropoda) Adult olfactory receptor neuron or47b Lamina monopolar neuron l4 Spermatogonium Cyst cell of testis Spermatocyte cyst cell Adult dopaminergic pam neuron Mechanosensory neuron Enterocyte of anterior adult midgut epithelium Compound eye cone cell Copper cell Photoreceptor cell r8 T2a neuron

Insect adult thorax Male reproductive gland Open tracheal system trachea Dorsal vessel heart Insect proboscis Malpighian tubule Post-embryonic organism Imaginal disc-derived wing Haltere Digestive tract Arthropod fat body Insect leg Antenna Panarthropod head Testis Body wall Ovary

Day 2 of adulthood Day 5 of adulthood Day 3 of adulthood Day 1 of adulthood

Normal

Female Male Mixed sex

10x genomics v3

Mus musculus

Endocardial cell Endothelial cell of lymphatic vessel Pericyte Glomerular endothelial cell Endothelial cell of hepatic sinusoid Cerebral cortex endothelial cell Vein endothelial cell Microvascular endothelial cell Endothelial cell Embryonic blood vessel endothelial progenitor cell Endothelial cell of artery Brain pericyte

Embryo

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

Normal

Female Male

Sci-rna-seq3

Nucleus