Homo sapiens

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

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

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

Normal

Female Male

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

Cell Nucleus

Mus musculus

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

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

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

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

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

Blood

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

Cytomegalovirus infection Normal

Female Male

10x 3' v3

Cell

Homo sapiens

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

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

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

Normal

Female Male

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

Cell Nucleus

Homo sapiens

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

Blood

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

Normal

Male

10x 3' v3

Cell

Mus musculus

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

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

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

Blood

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

Normal

Male

10x 3' v3

Cell

Homo sapiens

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

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

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

Normal

10x 3' v3 10x 3' v2

Cell

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 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

66-year-old stage 69-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 13-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 2-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 14-year-old 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 25-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 18-year-old stage 31-year-old stage 36-year-old stage Fourth decade stage 22-year-old stage Newborn stage (0-28 days) 63-year-old stage 20-year-old stage Carnegie stage 16 Eighth decade stage 76-year-old stage Prime adult stage 5-year-old stage 11-year-old 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)

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

Female Male

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

Cell

Mus musculus

Cell

Normal

Dronc-seq Merfish 10x 3' v2

Macaca mulatta

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

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