Homo sapiens

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

Blood

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

Cytomegalovirus infection

Female

10x 3' v3

Cell

Macaca mulatta

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

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

Prime adult stage Juvenile stage

Normal

Male Female

Sci-rna-seq3

Nucleus

Homo sapiens

Neuron Leukocyte

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

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

Normal

Male Female

10x 3' v3

Nucleus

Homo sapiens

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

Respiratory airway Lung parenchyma Nose Lung

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

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

Male Female

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

Cell Nucleus

Homo sapiens

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

Breast

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

Normal

Female

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

Cell

Mus musculus

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

Embryo

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

Normal

Male Female

Sci-rna-seq3

Nucleus

Homo sapiens

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

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

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

Parkinson disease Normal

Male Female

10x 3' v3

Nucleus

Mus musculus

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

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

9-week-old stage

Normal

Female

Merfish

Mus musculus

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

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

9-week-old stage

Normal

Female

Merfish

Mus musculus

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

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

9-week-old stage

Normal

Male

Merfish

Mus musculus

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

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

9-week-old stage

Normal

Male

Merfish

Homo sapiens

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

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

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

Normal

Male Female

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

Cell Nucleus