Homo sapiens

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

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

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

Normal

Female Male

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

Cell Nucleus

Mus musculus

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

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

9-week-old stage

Normal

Male

Merfish

Mus musculus

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

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

9-week-old stage

Normal

Male

Merfish

Homo sapiens

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

Blood

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

Normal Cytomegalovirus infection

Female Male

10x 3' v3

Cell

Homo sapiens

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

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

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

Normal

Female Male

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

Cell Nucleus

Homo sapiens

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

Blood

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

Normal

Male

10x 3' v3

Cell

Mus musculus

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

Embryo

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

Normal

Female Male

Sci-rna-seq3

Nucleus

Homo sapiens

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

Blood

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

Normal

Male

10x 3' v3

Cell

Homo sapiens

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

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

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

Normal

10x 3' v2 10x 3' v3

Cell

Homo sapiens

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

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

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

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

Female Male

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

Cell

Mus musculus

Cell

Normal

10x 3' v2 Merfish Dronc-seq

Macaca mulatta

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

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

Juvenile stage Prime adult stage

Normal

Female Male

Sci-rna-seq3

Nucleus