Mus musculus

Astrocyte Dopaminergic neuron Neuroblast (sensu vertebrata) Histaminergic neuron Gabaergic neuron Glycinergic neuron Smooth muscle cell Oligodendrocyte precursor cell Oligodendrocyte Dendritic cell Olfactory ensheathing cell Hypendymal cell Bergmann glial cell Cholinergic neuron Pericyte Lymphocyte Ependymal cell Glutamatergic neuron Macrophage Tanycyte Monocyte Vascular leptomeningeal cell Microglial cell Choroid plexus epithelial cell Endothelial cell

Midbrain Striatum Neocortex Cortical subplate Hypothalamus Brain Pallidum Cerebellum Hippocampal formation White matter Hindbrain Thalamic complex Ventricular system of brain

9-week-old stage

Normal

Male

Merfish

Mus musculus

Astrocyte Dopaminergic neuron Neuroblast (sensu vertebrata) Histaminergic neuron Gabaergic neuron Glycinergic neuron Smooth muscle cell Oligodendrocyte precursor cell Oligodendrocyte Dendritic cell Olfactory ensheathing cell Hypendymal cell Bergmann glial cell Cholinergic neuron Pericyte Lymphocyte Ependymal cell Glutamatergic neuron Macrophage Tanycyte Monocyte Vascular leptomeningeal cell Microglial cell Choroid plexus epithelial cell Endothelial cell

Midbrain Striatum Neocortex Cortical subplate Hypothalamus Brain Pallidum Cerebellum Hippocampal formation White matter Hindbrain Thalamic complex Ventricular system of brain

9-week-old stage

Normal

Male

Merfish

Homo sapiens

Innate lymphoid cell Effector memory cd4-positive, alpha-beta t cell Basophil mast progenitor cell Double negative thymocyte Mucosal invariant t cell Common myeloid progenitor Cd16-positive, cd56-dim natural killer cell, human Effector memory cd8-positive, alpha-beta t cell Cd14-low, cd16-positive monocyte Be cell Intermediate monocyte Central memory cd4-positive, alpha-beta t cell Cd4-positive, alpha-beta memory t cell Cd141-positive myeloid dendritic cell Memory b cell Plasma cell Cd14-positive, cd16-negative classical monocyte Mature gamma-delta t cell Axl+ dendritic cell, human Cd1c-positive myeloid dendritic cell Naive thymus-derived cd4-positive, alpha-beta t cell Cd8-positive, alpha-beta regulatory t cell Naive thymus-derived cd8-positive, alpha-beta t cell Plasmacytoid dendritic cell Memory regulatory t cell Cd16-negative, cd56-bright natural killer cell, human Central memory cd8-positive, alpha-beta t cell Natural killer cell Platelet Erythrocyte Cd8-positive, alpha-beta memory t cell T cell Cd8aa(i) thymocyte Naive b cell Memory ccr4-positive regulatory t cell Naive regulatory t cell Transitional stage b cell Common lymphoid progenitor

Blood

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

Cytomegalovirus infection Normal

Female Male

10x 3' v3

Cell

Homo sapiens

Cerebral cortex pyramidal neuron L6b glutamatergic cortical neuron Premigratory neural crest cell Neural progenitor cell Astrocyte Neurectodermal cell Extratelencephalic-projecting glutamatergic cortical neuron Neuroblast (sensu vertebrata) Cerebellar granule cell Gabaergic neuron Glial cell Cerebellar neuron Amacrine cell Pluripotent stem cell Immature astrocyte Retinal progenitor cell Fibroblast of choroid plexus Glioblast Oligodendrocyte precursor cell Epithelial cell Caudal ganglionic eminence derived interneuron Cerebellum glutamatergic neuron Cerebral cortex neuron Midbrain dopaminergic neuron Pyramidal neuron Purkinje cell Mesenchymal cell Pigmented epithelial cell Bergmann glial cell Medial ganglionic eminence derived gabaergic interneuron Central nervous system neuron Neuroepithelial stem cell Extracellular matrix secreting cell Interneuron Mesodermal cell Neural cell Mature astrocyte Hypothalamus cell Neuron of the forebrain Glutamatergic neuron Neuroplacodal cell Cajal-retzius cell Cerebral cortex gabaergic interneuron Forebrain neuroblast Gabaergic interneuron Neural crest derived neuron Neural stem cell Medium spiny neuron Radial glial cell Sst gabaergic interneuron Ciliated cell Mueller cell Forebrain radial glial cell Microglial cell Choroid plexus epithelial cell Eye photoreceptor cell Neuron Neural crest cell Stem cell Endothelial cell

Midbrain tectum Cerebral cortex Midbrain tegmentum Brain Cerebellum Choroid plexus Telencephalon Arcuate nucleus of hypothalamus Hindbrain Ventral part of telencephalon Dorsal plus ventral thalamus

27-year-old stage Blastula stage Third decade stage Sixth decade stage Newborn stage (0-28 days) 36-year-old stage 4-year-old stage Fourth decade stage 48-year-old stage 30-year-old stage 55-year-old stage 58-year-old stage 22-year-old stage Fifth decade stage 63-year-old stage 25-year-old stage Seventh decade stage

Normal

Female Male

Bd rhapsody whole transcriptome analysis 10x multiome 10x 3' v3 Quartz-seq Split-seq Drop-seq Smart-seq2 10x 3' v2

Cell Nucleus

Homo sapiens

Innate lymphoid cell Effector memory cd4-positive, alpha-beta t cell Basophil mast progenitor cell Double negative thymocyte Mucosal invariant t cell Common myeloid progenitor Cd16-positive, cd56-dim natural killer cell, human Effector memory cd8-positive, alpha-beta t cell Cd14-low, cd16-positive monocyte Be cell Intermediate monocyte Central memory cd4-positive, alpha-beta t cell Cd4-positive, alpha-beta memory t cell Cd141-positive myeloid dendritic cell Memory b cell Plasma cell Cd14-positive, cd16-negative classical monocyte Mature gamma-delta t cell Axl+ dendritic cell, human Cd1c-positive myeloid dendritic cell Naive thymus-derived cd4-positive, alpha-beta t cell Cd8-positive, alpha-beta regulatory t cell Naive thymus-derived cd8-positive, alpha-beta t cell Plasmacytoid dendritic cell Memory regulatory t cell Cd16-negative, cd56-bright natural killer cell, human Central memory cd8-positive, alpha-beta t cell Natural killer cell Platelet Erythrocyte Cd8-positive, alpha-beta memory t cell T cell Cd8aa(i) thymocyte Naive b cell Memory ccr4-positive regulatory t cell Naive regulatory t cell Transitional stage b cell Common lymphoid progenitor

Blood

62-year-old stage 61-year-old stage 57-year-old stage 59-year-old stage 55-year-old stage 64-year-old stage 66-year-old stage 63-year-old stage 60-year-old stage 56-year-old stage 67-year-old stage 65-year-old stage

Normal

Male

10x 3' v3

Cell

Mus musculus

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

Embryo

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

Normal

Female Male

Sci-rna-seq3

Nucleus

Homo sapiens

Innate lymphoid cell Effector memory cd4-positive, alpha-beta t cell Basophil mast progenitor cell Double negative thymocyte Mucosal invariant t cell Common myeloid progenitor Cd16-positive, cd56-dim natural killer cell, human Effector memory cd8-positive, alpha-beta t cell Cd14-low, cd16-positive monocyte Be cell Intermediate monocyte Central memory cd4-positive, alpha-beta t cell Cd4-positive, alpha-beta memory t cell Cd141-positive myeloid dendritic cell Memory b cell Plasma cell Cd14-positive, cd16-negative classical monocyte Mature gamma-delta t cell Axl+ dendritic cell, human Cd1c-positive myeloid dendritic cell Naive thymus-derived cd4-positive, alpha-beta t cell Cd8-positive, alpha-beta regulatory t cell Naive thymus-derived cd8-positive, alpha-beta t cell Plasmacytoid dendritic cell Memory regulatory t cell Cd16-negative, cd56-bright natural killer cell, human Central memory cd8-positive, alpha-beta t cell Natural killer cell Platelet Erythrocyte Cd8-positive, alpha-beta memory t cell T cell Cd8aa(i) thymocyte Naive b cell Memory ccr4-positive regulatory t cell Naive regulatory t cell Transitional stage b cell Common lymphoid progenitor

Blood

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

Normal

Male

10x 3' v3

Cell

Homo sapiens

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

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

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

Normal

10x 3' v3 10x 3' v2

Cell

Homo sapiens

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

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

54-year-old stage 35-year-old stage Adult stage 39-year-old stage 62-year-old stage Carnegie stage 19 74-year-old stage 26-year-old stage 72-year-old stage 9-year-old stage 21st week post-fertilization stage Third decade stage Carnegie stage 18 10th week post-fertilization stage 21-year-old stage 85-year-old stage 81-year-old stage 61-year-old stage 57-year-old stage Juvenile stage (5-14 yo) 13-year-old stage Sixth decade stage Newborn stage (0-28 days) 36-year-old stage Embryonic stage 4-year-old stage 16th week post-fertilization stage Fourth decade stage 52-year-old stage 86-year-old stage 48-year-old stage Carnegie stage 22 19th week post-fertilization stage 70-year-old stage 6-year-old stage 12-year-old stage 45-year-old stage 41-year-old stage 59-year-old stage Eighth decade stage 30-year-old stage 10-year-old stage 2-month-old stage 55-year-old stage 23-year-old stage 58-year-old stage 14-year-old stage 2-year-old stage 75-year-old stage 22-year-old stage 18-year-old stage 50-year-old stage 51-year-old stage 68-year-old stage 29-year-old stage 66-year-old stage 15th week post-fertilization stage 77-year-old stage 11-year-old stage 11th week post-fertilization stage 13th week post-fertilization stage 33-year-old stage 69-year-old stage 32-year-old stage 12th week post-fertilization stage 28-year-old stage 76-year-old stage Young adult stage 5-year-old stage Fifth decade stage 31-year-old stage Carnegie stage 17 87-year-old stage 63-year-old stage 60-year-old stage 80-year-old stage Prime adult stage 18th week post-fertilization stage 84-year-old stage 25-year-old stage 56-year-old stage 37-year-old stage Pediatric stage 9th week post-fertilization stage 46-year-old stage 24-year-old stage 67-year-old stage 43-year-old stage 20-year-old stage 65-year-old stage 17th week post-fertilization stage Seventh decade stage 44-year-old stage 34-year-old stage Carnegie stage 16

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

Female Male

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

Cell

Mus musculus

Cell

Normal

Dronc-seq Merfish 10x 3' v2

Macaca mulatta

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

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

Prime adult stage Juvenile stage

Normal

Female Male

Sci-rna-seq3

Nucleus

Homo sapiens

L6b glutamatergic neuron of the primary motor cortex Astrocyte Lamp5 gabaergic interneuron L6 intratelencephalic projecting glutamatergic neuron Gabaergic neuron Smooth muscle cell L2/3 intratelencephalic projecting glutamatergic neuron Vip gabaergic interneuron Oligodendrocyte precursor cell L2/3-6 intratelencephalic projecting glutamatergic neuron Plasma cell Oligodendrocyte B cell L6 corticothalamic-projecting glutamatergic cortical neuron Pericyte L5/6 near-projecting glutamatergic neuron Pvalb gabaergic interneuron Natural killer cell Sst gabaergic interneuron Perivascular macrophage L5 extratelencephalic projecting glutamatergic cortical neuron Vascular leptomeningeal cell Microglial cell T cell Endothelial cell

Dorsolateral prefrontal cortex

54-year-old stage 35-year-old stage 39-year-old stage 62-year-old stage 27-year-old stage 78-year-old stage 73-year-old stage 74-year-old stage 26-year-old stage 53-year-old stage 19-year-old stage 21-year-old stage 83-year-old stage 85-year-old stage 61-year-old stage 57-year-old stage 13-year-old stage 49-year-old stage 42-year-old stage 1-month-old stage 36-year-old stage 17-year-old stage 4-year-old stage 52-year-old stage 48-year-old stage 6-year-old stage 40-year-old stage 12-year-old stage 38-year-old stage 45-year-old stage 41-year-old stage 59-year-old stage 3-year-old stage 30-year-old stage 10-year-old stage 2-month-old stage 55-year-old stage 23-year-old stage 58-year-old stage 3-month-old stage 14-year-old stage 2-year-old stage 75-year-old stage 22-year-old stage 15-year-old stage 18-year-old stage 50-year-old stage 51-year-old stage 79-year-old stage 68-year-old stage 29-year-old stage 66-year-old stage 33-year-old stage 32-year-old stage 28-year-old stage 76-year-old stage 4-month-old stage 5-year-old stage 31-year-old stage 8-year-old stage 63-year-old stage 60-year-old stage 84-year-old stage 25-year-old stage 56-year-old stage 37-year-old stage 46-year-old stage 24-year-old stage 6-month-old stage 67-year-old stage 43-year-old stage 20-year-old stage 65-year-old stage 71-year-old stage 44-year-old stage 34-year-old stage 16-year-old stage 47-year-old stage

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

Female Male

10x 3' v3

Nucleus