Homo sapiens

T cell Effector cd8-positive, alpha-beta t cell Germinal center b cell Granulocyte Endothelial tip cell Mature conventional dendritic cell Endothelial cell of venule Natural killer cell Endothelial cell of lymphatic vessel Gamma-delta t cell Activated cd4-positive, alpha-beta t cell Mature nk t cell Colon endothelial cell Mast cell Cd8-positive, alpha-beta t cell Iga plasma cell Stem cell Endothelial cell of artery Capillary endothelial cell Schwann cell Smooth muscle cell Plasmacytoid dendritic cell Igg plasma cell Enteroendocrine cell Cd8-positive, alpha-beta memory t cell Group 3 innate lymphoid cell Goblet cell T-helper 17 cell Macrophage Tuft cell of colon Cd4-positive, cd25-positive, alpha-beta regulatory t cell Mature b cell Enterocyte Intestinal epithelial cell Cd4-positive, alpha-beta t cell Glandular secretory epithelial cell T follicular helper cell Colon goblet cell Pericyte Monocyte Myofibroblast cell Conventional dendritic cell Fibroblast Colonocyte Dendritic cell

Colorectum

69-year-old stage 91-year-old stage 42-year-old stage 89-year-old stage 71-year-old stage 53-year-old stage 61-year-old stage 52-year-old stage 48-year-old stage 56-year-old stage 55-year-old stage 84-year-old stage 82-year-old stage 50-year-old stage 90-year-old stage 51-year-old stage 57-year-old stage 72-year-old stage 81-year-old stage 49-year-old stage 35-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 70-year-old stage 60-year-old stage 78-year-old stage 36-year-old stage 47-year-old stage 76-year-old stage 73-year-old stage

Normal Colon adenocarcinoma

Female Male

10x 3' v2 10x 3' v3

Cell

Mus musculus

Endothelial cell of hepatic sinusoid Kidney cell T cell Neutrophil Bladder urothelial cell Endocardial cell Club cell Granulocyte Tuft cell of large intestine Neural stem cell Hepatocyte Stromal cell Immature t cell Natural killer cell Endothelial cell of lymphatic vessel Erythrocyte Oligodendrocyte precursor cell Multiciliated columnar cell of tracheobronchial tree Mature alpha-beta t cell Secretory cell Kidney collecting duct epithelial cell Endothelial cell Kupffer cell Oligodendrocyte Cardiac valve cell Neuroendocrine cell Mature nk t cell Hematopoietic precursor cell Erythroid progenitor cell, mammalian Kidney interstitial fibroblast Mast cell Kidney cortex artery cell Cd8-positive, alpha-beta t cell Pulmonary neuroendocrine cell Pancreatic acinar cell Pancreatic pp cell Late pro-b cell Basal cell Stem cell of epidermis Luminal epithelial cell of mammary gland Bladder cell Schwann cell Leukocyte Classical monocyte Kidney capillary endothelial cell Smooth muscle cell Intermediate monocyte Epithelial cell of proximal tubule Epithelial cell Smooth muscle cell of the pulmonary artery Skeletal muscle satellite cell Dn3 thymocyte Plasmacytoid dendritic cell Cardiac neuron Precursor b cell Lymphoid lineage restricted progenitor cell Hepatic stellate cell Pancreatic a cell Myeloid dendritic cell Immature nk t cell Enteroendocrine cell Brain pericyte Plasmatocyte Lymphocyte Lung macrophage Thymocyte Basal cell of epidermis Ependymal cell Tuft cell Endothelial cell of coronary artery Macrophage Intestinal crypt stem cell Microglial cell Fenestrated endothelial cell Pancreatic d cell Kidney distal convoluted tubule epithelial cell Kidney collecting duct principal cell Regulatory t cell Macrophage dendritic cell progenitor Pulmonary alveolar type 1 cell Pancreatic stellate cell Duct epithelial cell Kidney loop of henle thick ascending limb epithelial cell Myeloid cell Bronchial smooth muscle cell Respiratory basal cell Promonocyte Fibroblast of lung Keratinocyte Hematopoietic stem cell Kidney proximal straight tubule epithelial cell Alveolar macrophage Plasma cell Cd4-positive, alpha-beta t cell Vein endothelial cell Type b pancreatic cell Mesenchymal cell Mesangial cell Langerhans cell Interneuron Aortic endothelial cell Mesenchymal stem cell of adipose tissue Granulocytopoietic cell Epidermal cell Cell of skeletal muscle Pulmonary interstitial fibroblast Bergmann glial cell Keratinocyte stem cell Cardiac muscle cell B cell Pericyte Granulocyte monocyte progenitor cell Dn4 thymocyte Professional antigen presenting cell Naive t cell Circulating fibrocyte Neuron Mesenchymal stem cell Immature b cell Megakaryocyte-erythroid progenitor cell Neuroepithelial stem cell Smooth muscle cell of trachea Myeloid leukocyte Regular atrial cardiac myocyte Adventitial cell Monocyte Mucus secreting cell Naive b cell Kidney loop of henle ascending limb epithelial cell Pancreatic ductal cell Large intestine goblet cell Enterocyte of epithelium of large intestine Double negative thymocyte Erythroblast Blood cell Proerythroblast Astrocyte Basophil Epithelial cell of large intestine Epithelial cell of thymus Kidney proximal convoluted tubule epithelial cell Regular ventricular cardiac myocyte Fibroblast Early pro-b cell Dendritic cell Fibroblast of cardiac tissue Pulmonary alveolar type 2 cell Medium spiny neuron Non-classical monocyte Basal epithelial cell of tracheobronchial tree Chondrocyte

Skin of body Lung Thymus Brown adipose tissue Gonadal fat pad Diaphragm Mesenteric fat pad Trachea Aorta Liver Subcutaneous adipose tissue Kidney Heart Tongue Mammary gland Brain Pancreas Large intestine Limb muscle Spleen Bladder lumen Bone marrow Adipose tissue

4-week-old stage 3-month-old stage 20-month-old stage and over 18-month-old stage

Normal

Female Male

10x 3' v2 Smart-seq2

Cell

Homo sapiens

T cell Effector cd8-positive, alpha-beta t cell Endothelial cell Mature nk t cell Mast cell Cd8-positive, alpha-beta t cell Melanocyte Plasmacytoid dendritic cell, human Lymphocyte Naive thymus-derived cd8-positive, alpha-beta t cell T-helper 17 cell Macrophage Activated cd8-positive, alpha-beta t cell, human Microglial cell Regulatory t cell Myeloid cell Plasma cell Cd4-positive, alpha-beta t cell Hematopoietic multipotent progenitor cell Malignant cell T follicular helper cell B cell Naive t cell Monocyte Central memory cd8-positive, alpha-beta t cell Myofibroblast cell Epithelial cell of thymus Cd8-positive, cd28-negative, alpha-beta regulatory t cell Fibroblast Dendritic cell

Skin of body Skin of neck Skin of calf Breast Liver Kidney Skin of cheek Skin of external ear Skin of forehead Skin of knee Arm skin Brain Skin of scalp Nose skin

69-year-old stage 37-year-old stage Middle aged stage 65-year-old stage 43-year-old stage Sixth decade stage 71-year-old stage 85-year-old stage 61-year-old stage 52-year-old stage 54-year-old stage 68-year-old stage Fifth decade stage 80-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 Seventh decade stage 58-year-old stage Adult stage 67-year-old stage Late adult stage 77-year-old stage 64-year-old stage Postnatal stage 62-year-old stage 86-year-old stage 41-year-old stage 60-year-old stage 60-79 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 Prime adult stage

Melanoma Metastatic melanoma Estrogen-receptor positive breast cancer Her2 positive breast carcinoma Squamous cell carcinoma Triple-negative breast carcinoma Nonpapillary renal cell carcinoma Intrahepatic cholangiocarcinoma Hepatocellular carcinoma Basal cell carcinoma

Female Male

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

Cell

Homo sapiens

Stromal cell Ciliated cell Endothelial cell Colon endothelial cell Interstitial cell of cajal Stem cell Basal cell Schwann cell Smooth muscle cell Paneth cell Epithelial cell Intestinal tuft cell Enteroendocrine cell Mesodermal cell Goblet cell Enterocyte Mesothelial cell Pericyte Neuron Colon epithelial cell Hematopoietic cell M cell of gut

Duodenum Ileum Colon Intestine

Normal

10x 3' v2 10x 3' v3 10x 5' v2 Sort-seq Seq-well s3

Nucleus Cell

Homo sapiens

Mammary gland epithelial cell Luminal epithelial cell of mammary gland Luminal adaptive secretory precursor cell of mammary gland Basal-myoepithelial cell of mammary gland Luminal hormone-sensing cell of mammary gland

Breast

37-year-old stage 21-year-old stage 34-year-old stage 65-year-old stage 53-year-old stage 52-year-old stage 48-year-old stage 30-year-old stage 39-year-old stage 29-year-old stage 38-year-old stage 56-year-old stage 55-year-old stage 28-year-old stage 57-year-old stage 24-year-old stage 23-year-old stage 35-year-old stage 58-year-old stage 59-year-old stage 25-year-old stage 33-year-old stage 45-year-old stage 62-year-old stage 41-year-old stage 46-year-old stage 31-year-old stage 36-year-old stage 19-year-old stage 63-year-old stage 20-year-old stage 27-year-old stage 40-year-old stage

Normal

Female

10x 3' v3

Cell

Homo sapiens

Podocyte Migratory dendritic cell Natural killer cell Parietal epithelial cell 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 resident macrophage Kidney collecting duct intercalated cell Classical monocyte Epithelial cell of proximal tubule Plasmacytoid dendritic cell, human Neural cell 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 loop of henle thick ascending limb epithelial cell Plasma cell Naive regulatory t cell Cd8-alpha-negative thymic conventional dendritic cell B cell Naive thymus-derived cd4-positive, alpha-beta t cell Mucosal invariant t cell Kidney loop of henle thin ascending limb epithelial cell Effector memory cd8-positive, alpha-beta t cell Non-classical monocyte

Kidney

66-year-old stage 42-year-old stage Sixth decade 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

Homo sapiens

Tracheobronchial smooth muscle cell Neutrophil Lung megakaryocyte Airway submucosal gland collecting duct epithelial cell Mature conventional dendritic cell Ciliated cell Natural killer cell Lung secretory cell Secretory cell Mast cell Lung interstitial macrophage Alveolar capillary type 1 endothelial cell Pulmonary neuroendocrine cell Serous secreting cell Basal cell Endothelial cell of respiratory system lymphatic vessel Endothelial cell of artery Classical monocyte Ionocyte Plasmacytoid dendritic cell Myoepithelial cell Cd8-positive, alpha-beta cytotoxic t cell Goblet cell Brush cell of tracheobronchial tree Mesothelial cell of pleura Mucus secreting cell of tracheobronchial tree submucosal gland Innate lymphoid cell Regulatory t cell Deuterosomal cell Pulmonary alveolar type 1 cell Helper t cell Alveolar macrophage Plasma cell Vein endothelial cell Secondary crest myofibroblast Respiratory tract suprabasal cell Alveolar adventitial fibroblast Vein endothelial cell of respiratory system B cell Alveolar capillary type 2 endothelial cell Pericyte Alveolar type 1 fibroblast cell Vascular associated smooth muscle cell Conventional dendritic cell Pulmonary alveolar type 2 cell Non-classical monocyte Chondrocyte

Lung

66-year-old stage 69-year-old stage 37-year-old stage 75-year-old stage 21-year-old stage 13-year-old stage 65-year-old stage 42-year-old stage 26-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 17-year-old stage 29-year-old stage 38-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 12-year-old stage 72-year-old stage 49-year-old stage 24-year-old stage 23-year-old stage 35-year-old stage 59-year-old stage 25-year-old stage 67-year-old 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 31-year-old stage 36-year-old stage 22-year-old stage 63-year-old stage 20-year-old stage 47-year-old stage 76-year-old stage 79-year-old stage 27-year-old stage 40-year-old stage 10-year-old stage

Normal

Female Male

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

Cell

Mus musculus

T cell Cell Oligodendrocyte precursor cell Endothelial cell Oligodendrocyte Vascular leptomeningeal cell Inhibitory interneuron Macrophage Microglial cell Pericyte Neuron Astrocyte Medium spiny neuron

Striatum Cortical layer v Cortical layer vi Olfactory region Cortical layer ii/iii Corpus callosum Brain ventricle Pia mater

4-week-old stage 24-week-old stage 20-month-old stage and over

Normal

Female

Merfish

Homo sapiens

Off midget ganglion cell Retinal ganglion cell Off parasol ganglion cell On midget ganglion cell On parasol ganglion 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 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

L2/3-6 intratelencephalic projecting glutamatergic 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

Normal Dementia

Female Male

10x 3' v3 10x multiome

Nucleus

Homo sapiens

Natural killer cell Oligodendrocyte precursor cell Endothelial cell Oligodendrocyte Mast cell Macrophage Microglial cell Mural cell Radial glial cell Plasma cell Malignant cell B cell Mature t cell Neuron Monocyte Astrocyte Dendritic cell

Temporoparietal junction Left parietal lobe Frontal lobe Left frontal lobe Temporal lobe Right temporal lobe Brain Right parietal lobe Left temporal lobe Right frontal lobe Forebrain

66-year-old stage 69-year-old stage 21-year-old stage 34-year-old stage 65-year-old stage 42-year-old 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 44-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 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 70-year-old stage 46-year-old stage 60-year-old stage 78-year-old stage 36-year-old stage 63-year-old stage 76-year-old stage 83-year-old stage

Glioblastoma

Female Male

10x 3' v2 10x 3' v3 10x 5' v1 Bd rhapsody whole transcriptome analysis Cel-seq2 Strt-seq Smart-seq2 Microwell-seq

Cell

Homo sapiens

Central memory cd4-positive, alpha-beta t cell Gamma-delta t cell Effector memory cd4-positive, alpha-beta t cell Leukocyte Classical monocyte Plasmacytoid dendritic cell Effector memory cd4-positive, alpha-beta t cell, terminally differentiated Unswitched memory b cell 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 Plasma cell Hematopoietic multipotent progenitor cell Megakaryocyte Mucosal invariant t cell Central memory cd8-positive, alpha-beta t cell Naive b cell Conventional dendritic cell Class switched memory b cell Cd16-negative, cd56-bright natural killer cell, human Effector memory cd8-positive, alpha-beta t cell Non-classical monocyte

Blood

69-year-old stage 37-year-old stage 21-year-old stage 34-year-old stage 26-year-old stage Sixth decade stage 71-year-old stage 53-year-old stage 30-year-old stage 39-year-old stage 44-year-old stage 29-year-old stage 38-year-old stage 55-year-old stage 28-year-old stage 51-year-old stage 57-year-old stage 49-year-old stage 35-year-old stage Seventh decade stage 58-year-old stage 59-year-old stage Adult stage Late adult stage 32-year-old stage 33-year-old stage 64-year-old stage 45-year-old stage 62-year-old stage 70-year-old stage 46-year-old stage 22-year-old stage 63-year-old stage Eighth decade stage 73-year-old stage 27-year-old stage 40-year-old stage

Normal

Female Male

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

Cell