Homo sapiens

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

Blood

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

Cytomegalovirus infection

Female

10x 3' v3

Cell

Macaca mulatta

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

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

Prime adult stage Juvenile stage

Normal

Female Male

Sci-rna-seq3

Nucleus

Homo sapiens

Leukocyte Neuron

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

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

Normal

Female Male

10x 3' v3

Nucleus

Homo sapiens

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

Nose Lung Lung parenchyma Respiratory airway

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

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

Female Male

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

Cell Nucleus

Homo sapiens

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

Breast

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

Normal

Female

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

Cell

Mus musculus

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

Embryo

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

Normal

Female Male

Sci-rna-seq3

Nucleus

Homo sapiens

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

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

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

Parkinson disease Normal

Female Male

10x 3' v3

Nucleus

Mus musculus

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

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

9-week-old stage

Normal

Female

Merfish

Mus musculus

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

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

9-week-old stage

Normal

Female

Merfish

Mus musculus

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

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

9-week-old stage

Normal

Male

Merfish

Mus musculus

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

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

9-week-old stage

Normal

Male

Merfish

Homo sapiens

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

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

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

Normal

Female Male

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

Cell Nucleus