Mus musculus

Pyramidal neuron Central nervous system macrophage Glutamatergic neuron L4/5 intratelencephalic projecting glutamatergic neuron of the primary motor cortex Endothelial cell Oligodendrocyte Hippocampal neuron Meis2 expressing cortical gabaergic cell Vascular leptomeningeal cell (mmus) Lamp5 gabaergic interneuron Cajal-retzius cell L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex Vip gabaergic interneuron L2/3-6 intratelencephalic projecting glutamatergic neuron L5 extratelencephalic projecting glutamatergic cortical neuron L6b glutamatergic cortical neuron L6 corticothalamic-projecting glutamatergic cortical neuron Pvalb gabaergic interneuron Pericyte L2/3 intratelencephalic projecting glutamatergic neuron of the primary motor cortex Sncg gabaergic interneuron Sst chodl gabaergic interneuron Astrocyte L5/6 near-projecting glutamatergic neuron of the primary motor cortex Sst gabaergic interneuron Cortical interneuron Corticothalamic-projecting glutamatergic cortical neuron

Auditory cortex Parietal cortex Primary visual cortex Temporal cortex Frontal lobe Subicular complex Lateral visual area Entorhinal cortex Posterior parietal association areas Retrosplenial granular cortex Agranular insular cortex Primary somatosensory cortex Primary motor cortex Hippocampal formation Visual cortex Medial orbital frontal cortex Anterior cingulate cortex

9-week-old stage 7-week-old stage 8-week-old stage

Normal

Female Male

10x 3' v2

Cell

Homo sapiens

Fast muscle cell T cell Neutrophil Transit amplifying cell of small intestine Bladder urothelial cell Progenitor cell of mammary luminal epithelium Club cell Granulocyte Respiratory tract goblet cell Muscle cell Cardiac endothelial cell Serous cell of epithelium of bronchus Hepatocyte Stromal cell Intestinal crypt stem cell of colon Luminal cell of prostate epithelium Endothelial cell of venule Natural killer cell Endothelial cell of lymphatic vessel Erythroid progenitor cell Erythrocyte Enterocyte of epithelium proper of small intestine Multiciliated columnar cell of tracheobronchial tree Conjunctival epithelial cell Gamma-delta t cell Thymic fibroblast type 1 Tissue-resident macrophage Slow muscle cell Enterochromaffin-like cell Activated cd4-positive, alpha-beta t cell Best4+ enterocyte Endothelial cell Mature nk t cell Stromal cell of ovary Retinal ganglion cell Hematopoietic precursor cell Colon endothelial cell Retinal pigment epithelial cell Interstitial cell of cajal Mast cell Pulmonary ionocyte Corneal epithelial cell Cd8-positive, alpha-beta t cell Myo-medullary thymic epithelial cell Pancreatic acinar cell Platelet Pancreatic pp cell Endothelial cell of arteriole Colon macrophage Blood vessel smooth muscle cell Tendon cell Myometrial cell Basal cell Luminal epithelial cell of mammary gland Erythroid lineage cell Endothelial cell of artery Capillary endothelial cell Schwann cell Taste receptor cell Melanocyte Leukocyte Classical monocyte Ionocyte Smooth muscle cell Thymic fibroblast type 2 Intermediate monocyte Enteroglial cell Epithelial cell Connective tissue cell Intestinal tuft cell Plasmacytoid dendritic cell Hepatic stellate cell Pancreatic a cell Myeloid dendritic cell Enteroendocrine cell Lung multiciliated epithelial cell Vestibular dark cell Enterocyte of epithelium proper of jejunum Endothelial cell of vascular tree Myoepithelial cell Ovarian surface epithelial cell Adipocyte Enterocyte of epithelium proper of duodenum Small intestine goblet cell Naive thymus-derived cd8-positive, alpha-beta t cell Thymocyte Retinal bipolar neuron Transit amplifying cell of colon Macrophage Tuft cell of colon Microglial cell Pancreatic d cell Paneth cell of colon Peritubular myoid cell Innate lymphoid cell Regulatory t cell Neuro-medullary thymic epithelial cell Pulmonary alveolar type 1 cell Mural cell Pancreatic stellate cell Paneth cell of epithelium of small intestine Duct epithelial cell Radial glial cell Activated cd8-positive, alpha-beta t cell Myeloid cell Bronchial smooth muscle cell Ventricular cardiac muscle cell Enteroendocrine cell of small intestine Tongue muscle cell Fibroblast of breast Spermatid Enterocyte of epithelium proper of ileum Hematopoietic stem cell Glial cell Acinar cell of salivary gland Common myeloid progenitor Plasma cell Cd4-positive, alpha-beta t cell Vein endothelial cell Type b pancreatic cell Kidney epithelial cell Cd8-positive, alpha-beta thymocyte Mesenchymal cell Glandular secretory epithelial cell Retina horizontal cell Cd4-positive, alpha-beta thymocyte Langerhans cell Oocyte T follicular helper cell Alveolar adventitial fibroblast Mesenchymal stem cell of adipose tissue Acinar cell Medullary thymic epithelial cell Epithelial cell of uterus Mesothelial cell Tracheal goblet cell Supporting cell of vestibular epithelium Ciliated epithelial cell Spermatocyte B cell Pericyte Mueller cell Naive thymus-derived cd4-positive, alpha-beta t cell Skeletal muscle satellite stem cell Male germ cell Serous cell of epithelium of trachea Neuron Mesenchymal stem cell Myeloid leukocyte Intestinal crypt stem cell of small intestine Regular atrial cardiac myocyte Adventitial cell Monocyte Eye photoreceptor cell Mucus secreting cell Vascular associated smooth muscle cell Pancreatic ductal cell Large intestine goblet cell Enterocyte of epithelium of large intestine Stratified squamous epithelial cell Myofibroblast cell Leydig cell Basophil Spermatogonium Epithelial fate stem cell Retinal blood vessel endothelial cell Fibroblast Theca cell Type l enteroendocrine cell Basal cell of prostate epithelium Fibroblast of cardiac tissue Sebocyte Hematopoietic cell Intrahepatic cholangiocyte Keratocyte Pulmonary alveolar type 2 cell Non-classical monocyte Mononuclear phagocyte Salivary gland cell

Inferior vena cava Skin of abdomen Skin of body Lung Ascending colon Heart right ventricle Thymus Brown adipose tissue Conjunctiva Stomach Testis Duodenum Inguinal lymph node Thoracic aorta Crista ampullaris Uterus Small intestine Anterior part of tongue Utricle of membranous labyrinth Exocrine pancreas Mucosa of stomach Left ovary Trachea Endometrium Aorta Coronary artery Cornea Sublingual gland Ileum Liver Endocrine pancreas Subcutaneous adipose tissue Ovary Right cardiac atrium Muscle of pelvic diaphragm Stomach smooth muscle Chorioretinal region Anterior segment of eyeball Cardiac ventricle Kidney Eye Right ovary Cardiac atrium Buccal mucosa Heart Abdominal aorta Tongue Sclera Muscularis mucosae of stomach Submandibular gland Mammary gland Jejunum Myometrium Posterior segment of eyeball Large intestine Eyelid Spleen Muscle of abdomen Retinal neural layer Cortex of kidney Left coronary artery Parotid gland Blood Ocular surface region Lacrimal gland Lymph node Posterior part of tongue Bladder organ Bone marrow Adipose tissue Skin of chest Sigmoid colon Vasculature Prostate gland Mesenteric lymph node

69-year-old stage 37-year-old stage 42-year-old stage 26-year-old stage 61-year-old stage 38-year-old stage 56-year-old stage 55-year-old stage 57-year-old stage 74-year-old stage 59-year-old stage 67-year-old stage 33-year-old stage 45-year-old stage 46-year-old stage 60-year-old stage 36-year-old stage 22-year-old stage 40-year-old stage

Normal

Female Male

10x 3' v3 10x 5' v2 Smart-seq2 Smart-seq3

Cell

Homo sapiens

Neutrophil 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 Occipital lobe Left frontal lobe Temporal lobe Right temporal lobe Parietal lobe Basal ganglion Brain Right parietal lobe Left temporal lobe Right frontal lobe Right occipital 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 24-year-old stage 35-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 Drop-seq Strt-seq Smart-seq2 Microwell-seq

Nucleus Cell

Macaca mulatta

Glutamatergic 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

Blood vessel endothelial cell Endothelial cell Mast cell Ciliary muscle cell Schwann cell Melanocyte Lymphocyte Non-pigmented ciliary epithelial cell Macrophage Pigmented ciliary epithelial cell Trabecular meshwork cell B cell Pericyte Fibroblast Myelinating schwann cell

Ciliary body Eye trabecular meshwork Uvea

66-year-old stage 69-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 61-year-old stage 52-year-old stage 54-year-old stage 68-year-old stage 30-year-old stage 44-year-old stage 17-year-old stage 56-year-old stage 15-year-old stage 82-year-old stage 50-year-old stage 51-year-old stage 57-year-old stage 72-year-old stage 81-year-old stage 80 year-old and over stage 24-year-old stage 16-year-old stage 58-year-old stage 67-year-old stage 77-year-old stage 64-year-old stage 62-year-old stage 70-year-old stage 46-year-old stage 60-year-old stage 78-year-old stage 18-year-old stage 63-year-old stage 20-year-old stage 47-year-old stage 76-year-old stage 73-year-old stage 27-year-old stage

Normal

Female Male

10x 3' v3

Nucleus

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 Vermiform appendix Epithelium of small intestine Pylorus Rectum Esophagus Jejunum Duodenal epithelium Transverse colon Periodontium Parotid gland Descending colon Sigmoid colon Labial gland Epithelium of stomach Mesenteric lymph node

66-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 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 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 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 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 31-year-old stage Fourth decade stage 22-year-old stage Newborn stage (0-28 days) 63-year-old stage Carnegie stage 16 Eighth decade stage 76-year-old stage Prime adult 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)

Normal

Female Male

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

Cell

Mus musculus musculus

Oligodendrocyte precursor cell Oligodendrocyte Ependymal cell Macrophage Microglial cell Brain microvascular endothelial cell Glial cell Neuron Astrocyte Fibroblast

Normal

10x 3' v3

Homo sapiens

Central memory cd4-positive, alpha-beta t cell T cell Cd1c-positive myeloid dendritic cell Natural killer cell Double negative t regulatory cell Erythrocyte Gamma-delta t cell Cd8-positive, alpha-beta t cell Platelet Cd141-positive myeloid dendritic cell Effector memory cd4-positive, alpha-beta t cell Plasmacytoid dendritic cell Cd8-positive, alpha-beta memory t cell Cd4-positive, alpha-beta cytotoxic t cell Cd8-positive, alpha-beta cytotoxic t cell Naive thymus-derived cd8-positive, alpha-beta t cell Memory b cell Cd16-positive, cd56-dim natural killer cell, human Innate lymphoid cell Regulatory t cell Mature b cell Plasma cell Cd4-positive, alpha-beta t cell Cd14-positive monocyte Cd14-low, cd16-positive monocyte B cell Naive thymus-derived cd4-positive, alpha-beta t cell Mucosal invariant t cell Monocyte Naive b cell Conventional dendritic cell Dendritic cell Cd16-negative, cd56-bright natural killer cell, human

Blood

66-year-old stage 69-year-old stage 37-year-old stage 75-year-old stage 21-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 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 29-year-old stage 38-year-old stage 56-year-old stage 55-year-old stage 50-year-old stage 28-year-old stage 51-year-old stage 57-year-old stage 72-year-old stage 49-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 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 46-year-old stage 60-year-old stage 31-year-old stage 36-year-old stage 22-year-old stage 19-year-old stage 63-year-old stage 47-year-old stage 73-year-old stage 27-year-old stage 40-year-old stage

Normal

Female Male

10x 5' v2

Cell

Mus musculus

Erythroid progenitor 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

Homo sapiens

Oligodendrocyte precursor cell Endothelial cell Oligodendrocyte Cerebellar golgi cell Microglial cell Granule cell Interneuron Molecular layer interneuron Bergmann glial cell Pericyte Purkinje cell Astrocyte Unipolar brush cell

Essential tremor Normal

Parse evercode whole transcriptome v2

Homo sapiens

Oligodendrocyte precursor cell Endothelial cell Oligodendrocyte Cerebellar golgi cell Microglial cell Granule cell Interneuron Molecular layer interneuron Bergmann glial cell Pericyte Purkinje cell Astrocyte Unipolar brush cell

Cerebellum

69-year-old stage 75-year-old stage 91-year-old stage 89-year-old stage 93-year-old stage 87-year-old stage 71-year-old stage 85-year-old stage 88-year-old stage 68-year-old stage 84-year-old stage 92-year-old stage 82-year-old stage 90-year-old stage 100-year-old stage 80-year-old stage 72-year-old stage 81-year-old stage 74-year-old stage 97-year-old stage 95-year-old stage 67-year-old stage 77-year-old stage 94-year-old stage 86-year-old stage 70-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

Essential tremor Normal

Female Male

Split-seq

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