Homo sapiens

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

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

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

Normal

Female Male

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

Cell Nucleus

Mus musculus

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

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

9-week-old stage

Normal

Male

Merfish

Mus musculus

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

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

9-week-old stage

Normal

Male

Merfish

Homo sapiens

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

Blood

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

Normal Cytomegalovirus infection

Female Male

10x 3' v3

Cell

Homo sapiens

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

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

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

Normal

Female Male

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

Cell Nucleus

Homo sapiens

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

Blood

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

Normal

Male

10x 3' v3

Cell

Mus musculus

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

Embryo

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

Normal

Female Male

Sci-rna-seq3

Nucleus

Homo sapiens

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

Blood

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

Normal

Male

10x 3' v3

Cell

Homo sapiens

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

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

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

Normal

10x 3' v3 10x 3' v2

Cell

Homo sapiens

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

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

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

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

Female Male

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

Cell

Mus musculus

Cell

Normal

Merfish 10x 3' v2 Dronc-seq

Macaca mulatta

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

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

Prime adult stage Juvenile stage

Normal

Female Male

Sci-rna-seq3

Nucleus