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 25-year-old stage 33-year-old stage 27-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 26-year-old stage 29-year-old stage

Normal

Female

10x 3' v3

Cell

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

57-year-old stage 62-year-old stage 60-year-old stage 64-year-old stage 65-year-old stage 63-year-old stage 59-year-old stage 56-year-old stage 58-year-old stage 61-year-old stage 55-year-old stage

Cytomegalovirus infection

Female

10x 3' v3

Cell

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

Homo sapiens

Leukocyte Neuron

Inferior frontal gyrus Middle temporal gyrus Putamen Brodmann (1909) area 24 Cerebellar vermis Posterior parahippocampal gyrus Anterior olfactory nucleus Brodmann (1909) area 38 Pretectal region Subicular complex Gray matter of midbrain Brodmann (1909) area 14 Brodmann (1909) area 19 Inferior temporal gyrus Hypothalamus Brodmann (1909) area 32 Cerebrocerebellum Dentate gyrus of hippocampal formation Lateral geniculate body Bed nucleus of stria terminalis Median tuberal portion Brodmann (1909) area 13 Primary somatosensory cortex Medial geniculate body Preoptic area Substantia innominata Perirhinal cortex Body of caudate nucleus Extrastriate cortex Lateral nuclear group of thalamus Dorsal tegmental nucleus Brodmann (1909) area 23 Centromedian nucleus of thalamus Brodmann (1909) area 35 Epithalamus Substantia nigra Central amygdaloid nucleus Rostral ca3 Granular insular cortex Agranular insular cortex Globus pallidus Basolateral amygdaloid nuclear complex Parabrachial nucleus Ventral anterior nucleus of thalamus Nucleus of dorsal thalamus Anterior cortical amygdaloid nucleus Anterior nuclear group Brodmann (1909) area 43 Primary auditory cortex Medial entorhinal cortex Red nucleus Corticomedial nuclear complex Lateral posterior nucleus of thalamus Brodmann (1909) area 46 Nucleus of medulla oblongata Supraoptic nucleus Uncal ca1 Cerebellar nuclear complex Temporal fusiform gyrus Lateral entorhinal cortex Brodmann (1909) area 25 Midbrain nucleus Primary motor cortex Pulvinar nucleus Pontine tegmentum Primary visual cortex Subthalamic nucleus Spinal cord Superior parietal cortex Hippocampal field Inferior olivary complex Piriform cortex Lateral amygdaloid nucleus Brodmann (1909) area 40 Claustrum of brain Midbrain tectum Mammillary body Pontine reticular formation Pontine nuclear group Medial dorsal nucleus of thalamus Retrosplenial region Nucleus accumbens Medial zone of hypothalamus Intralaminar nuclear group Accessory basal amygdaloid nucleus Superior temporal gyrus Septal nuclear complex Cuneus cortex

50-year-old stage 60-year-old stage 42-year-old stage 29-year-old stage

Normal

Female Male

10x 3' v3

Nucleus

Homo sapiens

Bronchus fibroblast of lung Myofibroblast cell Acinar cell Cd1c-positive myeloid dendritic cell Pulmonary alveolar type 1 cell Capillary endothelial cell Classical monocyte Endothelial cell of lymphatic vessel Epithelial cell of lower respiratory tract Cd4-positive, alpha-beta t cell Pulmonary alveolar type 2 cell Club cell Pulmonary neuroendocrine cell Non-classical monocyte Ionocyte Mesothelial cell Alveolar macrophage Brush cell of tracheobronchial tree Alveolar type 1 fibroblast cell Stromal cell Mast cell Tracheobronchial smooth muscle cell Multiciliated columnar cell of tracheobronchial tree Pulmonary artery endothelial cell Tracheobronchial serous cell Vein endothelial cell Nasal mucosa goblet cell Serous secreting cell Respiratory tract hillock cell Conventional dendritic cell Fibroblast Tracheobronchial goblet cell Hematopoietic stem cell Multiciliated epithelial cell B cell Cd8-positive, alpha-beta t cell Lung macrophage Lung pericyte Bronchial goblet cell Dendritic cell Plasma cell Pulmonary alveolar epithelial cell T cell Plasmacytoid dendritic cell Mucus secreting cell Alveolar adventitial fibroblast Smooth muscle cell Respiratory basal cell Natural killer cell Elicited macrophage

Nose Lung Lung parenchyma Respiratory airway

66-year-old stage 16-year-old stage 79-year-old stage 6-month-old stage 70-year-old stage 3-month-old stage 18-year-old stage Fourth decade stage 77-year-old stage 21-year-old stage 50-year-old stage 86-year-old stage 57-year-old stage 76-year-old stage 62-year-old stage 46-year-old stage 52-year-old stage 60-year-old stage 22-year-old stage 44-year-old stage 48-year-old stage 64-year-old stage 45-year-old stage 25-year-old stage 33-year-old stage 65-year-old stage 67-year-old stage 2-year-old stage 11-month-old stage 40-year-old stage 1-month-old stage 12-month-old stage 75-year-old stage 27-year-old stage 23-year-old stage 37-year-old stage 71-year-old stage 14-year-old stage 36-year-old stage 63-year-old stage 59-year-old stage 54-year-old stage Fifth decade stage 20-year-old stage 47-year-old stage 31-year-old stage 56-year-old stage 58-year-old stage 68-year-old stage 61-year-old stage 15-year-old stage 34-year-old stage 51-year-old stage 49-year-old stage 42-year-old stage 35-year-old stage 53-year-old stage 10-year-old stage 72-year-old stage 73-year-old stage 30-year-old stage 24-year-old stage Seventh decade stage 3-year-old stage 26-year-old stage 12-year-old stage 7-year-old stage Newborn stage (0-28 days) 4-year-old stage 9-year-old stage 69-year-old stage 43-year-old stage 5-year-old stage 29-year-old stage 38-year-old stage 41-year-old stage 81-year-old stage 55-year-old stage Sixth decade stage

Pneumonia Chronic rhinitis Normal Lymphangioleiomyomatosis Lung large cell carcinoma Pleomorphic carcinoma Lung adenocarcinoma Chronic obstructive pulmonary disease Pulmonary sarcoidosis Hypersensitivity pneumonitis Cystic fibrosis Interstitial lung disease Pulmonary fibrosis Covid-19 Squamous cell lung carcinoma Non-specific interstitial pneumonia

Female Male

10x 5' v2 10x 5' v1 10x 3' v3 10x 5' transcription profiling 10x 3' v1 Seq-well Drop-seq 10x 3' v2

Cell Nucleus

Homo sapiens

Luminal hormone-sensing cell of mammary gland Capillary endothelial cell Naive b cell Innate lymphoid cell Endothelial cell of lymphatic vessel Class switched memory b cell Macrophage Naive thymus-derived cd4-positive, alpha-beta t cell Unswitched memory b cell Luminal adaptive secretory precursor cell of mammary gland Cd4-positive helper t cell Endothelial tip cell Perivascular cell Fibroblast of mammary gland Vein endothelial cell Tc1 cell Cd8-positive, alpha-beta memory t cell Effector memory cd8-positive, alpha-beta t cell Dendritic cell Plasma cell Mature nk t cell Basal-myoepithelial cell of mammary gland Natural killer cell Endothelial cell of artery Mammary gland epithelial cell

Breast

19-year-old stage 21-year-old stage 32-year-old stage 50-year-old stage 57-year-old stage 62-year-old stage Prime adult stage 46-year-old stage 52-year-old stage 22-year-old stage 44-year-old stage 48-year-old stage 45-year-old stage 25-year-old stage 33-year-old stage 65-year-old stage 40-year-old stage 27-year-old stage 23-year-old stage 37-year-old stage Adult stage 28-year-old stage 36-year-old stage 63-year-old stage 59-year-old stage 54-year-old stage 20-year-old stage 47-year-old stage 31-year-old stage 56-year-old stage 58-year-old stage 34-year-old stage 49-year-old stage 42-year-old stage 35-year-old stage 53-year-old stage 30-year-old stage 24-year-old stage 26-year-old stage 39-year-old stage 69-year-old stage 43-year-old stage 29-year-old stage 38-year-old stage 41-year-old stage 55-year-old stage

Normal

Female

10x 3' v3 10x 3' v1 10x 3' v2

Cell

Mus musculus

Small bistratified retinal ganglion cell Cerebral cortex gabaergic interneuron Glutamatergic neuron Gabaergic neuron Cranial motor neuron Neural progenitor cell Starburst amacrine cell Cajal-retzius cell Amacrine cell Spinal cord motor neuron Thalamic excitatory neuron Retinal ganglion cell Neuron Purkinje cell Retina horizontal 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

Glutamatergic neuron Mural cell Astrocyte Oligodendrocyte precursor cell Oligodendrocyte Gabaergic neuron Leukocyte Ependymal cell Endothelial cell Central nervous system neuron Central nervous system macrophage

Dorsal motor nucleus of vagus nerve Medial globus pallidus Primary motor cortex Primary visual cortex Prefrontal cortex

80-year-old stage 85-year-old stage 91-year-old stage 82-year-old stage 66-year-old stage 79-year-old stage 70-year-old stage 77-year-old stage 86-year-old stage 57-year-old stage 76-year-old stage 62-year-old stage 102-year-old stage 64-year-old stage 89-year-old stage 74-year-old stage 65-year-old stage 67-year-old stage 75-year-old stage 95-year-old stage 71-year-old stage 78-year-old stage 68-year-old stage 72-year-old stage 73-year-old stage 101-year-old stage 88-year-old stage 84-year-old stage 97-year-old stage 69-year-old stage 87-year-old stage 81-year-old stage 83-year-old stage

Normal Parkinson disease

Female Male

10x 3' v3

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 Thalamic complex Pallidum Brain Striatum Neocortex White matter Ventricular system of brain

9-week-old stage

Normal

Female

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

Female

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

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