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

Normal

Female

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

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

Cytomegalovirus infection

Female

10x 3' v3

Cell

Macaca mulatta

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

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

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

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

Normal

Female Male

10x 3' v3

Nucleus

Homo sapiens

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

Lung Lung parenchyma Nose Respiratory airway

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

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

Female Male

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

Cell Nucleus

Homo sapiens

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

Breast

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

Normal Precancerous condition

Female

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

Cell

Mus musculus

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

Embryo

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

Normal

Female Male

Sci-rna-seq3

Nucleus

Homo sapiens

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

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

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

Parkinson disease Normal

Female Male

10x 3' v3

Nucleus

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

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

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

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

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

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

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

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