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

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

9-week-old stage

Normal

Female

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

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

9-week-old stage

Normal

Female

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

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

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

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

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

66-year-old stage 37-year-old stage 75-year-old stage 21-year-old stage 34-year-old stage 65-year-old stage 42-year-old stage 43-year-old stage 71-year-old stage 53-year-old stage 61-year-old stage 52-year-old stage 54-year-old stage 68-year-old stage 48-year-old stage 39-year-old stage 44-year-old stage 38-year-old stage 56-year-old stage 55-year-old stage 50-year-old stage 28-year-old stage 51-year-old stage 57-year-old stage 72-year-old stage 74-year-old stage 24-year-old stage 23-year-old stage 35-year-old stage 58-year-old stage 59-year-old stage 67-year-old stage 32-year-old stage 33-year-old stage 64-year-old stage 45-year-old stage 62-year-old stage 41-year-old stage 70-year-old stage 46-year-old stage 60-year-old stage 78-year-old stage 31-year-old stage 36-year-old stage 22-year-old stage 63-year-old stage 47-year-old stage 76-year-old stage 73-year-old stage 40-year-old stage

Rheumatoid arthritis 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

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

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

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

Nucleus Cell

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

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

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

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

9-week-old stage

Normal

Male

Merfish

Homo sapiens

Central memory cd4-positive, alpha-beta t cell Intestinal crypt stem cell of colon Natural killer cell Granzyme k-associated cd8 t cell Gamma-delta t cell Tissue-resident macrophage Enterochromaffin-like cell Best4+ enterocyte Anorectum goblet cell Mast cell Platelet Cd8-positive, alpha-beta memory t cell, cd45ro-positive Classical monocyte Intermediate monocyte Intestinal tuft cell Plasmacytoid dendritic cell Subepithelial intestinal fibroblast Gut endothelial cell Naive thymus-derived cd8-positive, alpha-beta t cell Effector memory cd8-positive, alpha-beta t cell, terminally differentiated Cd4-positive, cd25-positive, alpha-beta regulatory t cell Memory b cell Innate lymphoid cell Paneth cell of epithelium of small intestine Best4+ colonocyte Intestinal enteroendocrine cell Plasmablast Enterocyte of epithelium proper of ileum Glial cell Plasma cell Cd4-positive, alpha-beta t cell Cd4-positive, alpha-beta memory t cell Ileal goblet cell B cell Pericyte Intestinal crypt stem cell of small intestine Monocyte Vascular associated smooth muscle cell Naive b cell Early colonocyte Myofibroblast cell Double negative thymocyte Conventional dendritic cell Fibroblast Colonocyte Cd4-positive, alpha-beta memory t cell, cd45ro-positive Effector memory cd8-positive, alpha-beta t cell Non-classical monocyte

Ileum Rectum Blood

Middle aged stage Adult stage 60-79 year-old stage Prime adult stage Young adult stage

Normal Crohn disease

Female Male

10x 3' v3

Cell

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

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

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

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

Nucleus Cell

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