Homo sapiens

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

Blood

26-year-old stage 35-year-old stage 29-year-old stage 34-year-old stage 31-year-old stage 25-year-old stage 36-year-old stage 32-year-old stage 28-year-old stage 30-year-old stage 27-year-old stage 33-year-old stage

Normal

Female

10x 3' v3

Cell

Homo sapiens

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

Blood

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

Cytomegalovirus infection

Female

10x 3' v3

Cell

Macaca mulatta

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

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

Homo sapiens

Unipolar brush cell Natural killer cell Medium spiny neuron Dentate gyrus granule cell Midbrain-derived inhibitory neuron Monocyte Near-projecting glutamatergic cortical neuron Intratelencephalic-projecting glutamatergic cortical neuron Cerebellar inhibitory gabaergic interneuron Medial ganglionic eminence derived interneuron Amygdala excitatory neuron Purkinje cell Mammillary body neuron T cell Thalamic excitatory neuron Hippocampal ca4 neuron Cerebral cortex neuron Hippocampal ca1-3 neuron Sst chodl gabaergic interneuron Cerebellar granule cell Caudal ganglionic eminence derived interneuron Lamp5 lhx6 neuron Neuron Pvalb chandelier gabaergic interneuron B cell Eccentric medium spiny neuron

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

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

Normal

Female Male

10x 3' v3

Nucleus

Homo sapiens

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

Lung Lung parenchyma Nose Respiratory airway

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

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

Female Male

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

Cell Nucleus

Homo sapiens

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

Breast

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

Normal

Female

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

Cell

Mus musculus

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

Embryo

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

Normal

Female Male

Sci-rna-seq3

Nucleus

Homo sapiens

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

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

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

Normal Parkinson disease

Female Male

10x 3' v3

Nucleus

Mus musculus

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

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

9-week-old stage

Normal

Female

Merfish

Mus musculus

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

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

Female

Merfish

Mus musculus

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

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

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

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