Mus musculus

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

Normal

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

Mus musculus

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

Optic cup Retina

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

Normal

Male

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

Cell

Homo sapiens

L2/3-6 intratelencephalic projecting glutamatergic neuron

Middle temporal gyrus

69-year-old stage 75-year-old stage 65-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 Adult 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

Normal Dementia

Female Male

10x multiome 10x 3' v3

Nucleus

Homo sapiens

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

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

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

Normal

Female Male

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

Cell

Homo sapiens

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

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

10x 3' v3 10x 3' v2

Homo sapiens

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

Blood

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

Cytomegalovirus infection Normal

Female Male

10x 3' v3

Cell

Homo sapiens

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

Decidua Placenta Blood Decidua basalis

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

Normal

Female

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

Cell Nucleus

Homo sapiens

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

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

Carnegie stage 19 13th week post-fertilization stage Carnegie stage 13 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 Carnegie stage 20 9th week post-fertilization stage Carnegie stage 23 10th week post-fertilization stage Carnegie stage 22 11th week post-fertilization stage

Normal

Female Male

10x 5' v1 10x 3' v2

Cell

Homo sapiens

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

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

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

Normal

Female Male

10x 5' transcription profiling 10x 3' v2

Cell

Mus musculus

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

Kidney

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

Normal Acute kidney failure

Female Male

10x multiome 10x 3' v2

Nucleus

Drosophila melanogaster

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

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

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

Normal

Mixed sex Female Male

10x genomics v3

Mus musculus

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

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