Mus musculus

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

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

9-week-old stage

Normal

Male

Merfish

Mus musculus

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

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

9-week-old stage

Normal

Male

Merfish

Homo sapiens

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

Blood

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

Cytomegalovirus infection Normal

Male Female

10x 3' v3

Cell

Homo sapiens

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

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

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

Normal

Male Female

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

Cell Nucleus

Homo sapiens

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

Blood

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

Normal

Male

10x 3' v3

Cell

Mus musculus

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

Embryo

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

Normal

Male Female

Sci-rna-seq3

Nucleus

Homo sapiens

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

Blood

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

Normal

Male

10x 3' v3

Cell

Homo sapiens

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

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

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

Normal

10x 3' v3 10x 3' v2

Cell

Homo sapiens

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

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

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

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

Male Female

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

Cell

Mus musculus

Cell

Normal

Dronc-seq Merfish 10x 3' v2

Macaca mulatta

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

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

Prime adult stage Juvenile stage

Normal

Male Female

Sci-rna-seq3

Nucleus

Homo sapiens

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

Dorsolateral prefrontal cortex

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

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

Male Female

10x 3' v3

Nucleus