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

66-year-old stage 75-year-old stage 21-year-old stage 34-year-old stage 65-year-old stage 42-year-old stage 43-year-old stage 61-year-old stage 52-year-old stage 68-year-old stage 48-year-old stage 44-year-old stage 56-year-old stage 57-year-old stage 74-year-old stage 23-year-old stage 35-year-old stage 58-year-old stage 59-year-old stage 67-year-old stage 32-year-old stage 33-year-old stage 45-year-old stage 62-year-old stage 46-year-old stage 60-year-old stage 31-year-old stage 36-year-old stage 22-year-old stage 47-year-old stage 76-year-old stage

Cytomegalovirus infection Normal

Female Male

10x 3' v3

Cell

Homo sapiens

T cell Diffuse bipolar 1 cell Diffuse bipolar 4b cell Gabaergic amacrine cell Blood vessel endothelial cell Off midget ganglion cell Diffuse bipolar 2 cell Endothelial cell of venule Natural killer cell Non-myelinating schwann cell Oligodendrocyte precursor cell Oligodendrocyte Retinal ganglion cell Retinal pigment epithelial cell Mast cell Off parasol ganglion cell Capillary endothelial cell Melanocyte Offx cell On midget ganglion cell Rod bipolar cell Retinal astrocyte S cone cell Adipocyte On parasol ganglion cell Invaginating midget bipolar cell Macrophage H2 horizontal cell Microglial cell Pigmented epithelial cell Fenestrated endothelial cell Diffuse bipolar 5 cell Retinal cone cell Glycinergic amacrine cell Retinal rod cell Flat midget bipolar cell Amacrine cell Diffuse bipolar 3a cell B cell Pericyte On-blue cone bipolar cell Diffuse bipolar 6 cell Mueller cell Giant bipolar cell Vascular associated smooth muscle cell Astrocyte Fibroblast Myelinating schwann cell Dendritic cell H1 horizontal cell Diffuse bipolar 4a cell Diffuse bipolar 3b cell

Cranial nerve ii Optic disc

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 43-year-old stage 71-year-old stage 85-year-old stage 53-year-old stage 61-year-old stage 52-year-old stage 54-year-old stage 68-year-old stage 30-year-old stage 17-year-old stage 56-year-old stage 15-year-old stage 82-year-old stage 50-year-old stage 72-year-old stage 81-year-old stage 74-year-old stage 16-year-old stage 58-year-old stage 25-year-old stage 67-year-old stage 90 year-old and over stage 3-year-old stage 32-year-old stage 77-year-old stage 33-year-old stage 64-year-old stage 45-year-old stage 62-year-old stage 70-year-old stage 46-year-old stage 60-year-old stage 18-year-old stage Newborn stage (0-28 days) 63-year-old stage 47-year-old stage 76-year-old stage 11-year-old stage 27-year-old stage 10-year-old stage

Normal

Female Male

10x 3' v3

Nucleus

Homo sapiens

Homo sapiens

Natural killer cell Endothelial cell of lymphatic vessel Endothelial cell Mast cell Endothelial cell of artery Capillary endothelial cell Smooth muscle cell Lymphocyte Adipocyte Myeloid cell Vein endothelial cell Mesothelial cell Cardiac muscle cell Pericyte Neuron Regular atrial cardiac myocyte Vascular associated smooth muscle cell Regular ventricular cardiac myocyte Fibroblast

Heart right ventricle Right cardiac atrium Apex of heart Heart left ventricle Left cardiac atrium Interventricular septum

66-year-old stage 75-year-old stage 21-year-old stage 65-year-old stage Sixth decade stage 71-year-old stage 61-year-old stage 52-year-old stage 54-year-old stage 68-year-old stage 48-year-old stage 39-year-old stage 44-year-old stage Fifth decade stage 55-year-old stage 51-year-old stage 35-year-old stage Seventh decade stage 59-year-old stage 62-year-old stage 46-year-old stage 60-year-old stage 63-year-old stage 20-year-old stage Eighth decade stage 47-year-old stage 73-year-old stage 27-year-old stage

Normal

Female Male

10x 3' v2 10x 3' v3 10x 5' v1

Nucleus Cell

Homo sapiens

T cell Fallopian tube secretory epithelial cell Endothelial cell Mast cell Plasma cell B cell Monocyte Fibroblast Dendritic cell

Ascitic fluid Diaphragm Caecum Peritoneum Parietal peritoneum Left ovary Liver Abdomen Urinary bladder Intestine Right ovary Adnexa of uterus Fallopian tube Large intestine Transverse colon Omentum Paracolic gutter Abdominal wall Lymph node

66-year-old stage 69-year-old stage 75-year-old stage 71-year-old stage 61-year-old stage 68-year-old stage 56-year-old stage 55-year-old stage 50-year-old stage 57-year-old stage 80 year-old and over stage 58-year-old stage 59-year-old stage 77-year-old stage 64-year-old stage 45-year-old stage 41-year-old stage 70-year-old stage 46-year-old stage 60-year-old stage 78-year-old stage 63-year-old stage 47-year-old stage 76-year-old stage

Malignant ovarian serous tumor

Female

10x 3' v3

Cell

Mus musculus

T cell Granulocyte Blood vessel endothelial cell Intestinal crypt stem cell of colon Cell Natural killer cell Endothelial cell of lymphatic vessel Mast cell Macrophage Regulatory t cell Malignant cell Colon glandular cell B cell Colon epithelial cell Monocyte Myofibroblast cell Fibroblast Colonocyte Dendritic cell Enteroendocrine cell of colon

Colorectal carcinoma Normal

10x 3' v2 10x 3' v3 Slide-seqv2 Spatial transcriptomics

Homo sapiens

T cell Granulocyte Cell Erythroid lineage cell Smooth muscle cell Innate lymphoid cell Myeloid cell Megakaryocyte Cell of skeletal muscle B cell Progenitor cell Fibroblast

Normal

10x 5' v2 10x 3' v2

Homo sapiens

T cell Osteoblast B-2 b cell Neutrophil Granulocyte Hepatocyte Stromal cell Natural killer cell Erythrocyte Small pre-b-ii cell Cd8-alpha-alpha-positive, alpha-beta intraepithelial t cell Endothelial cell B-1 b cell Kupffer cell Pro-b cell Interstitial cell of cajal Mast cell Late pro-b cell Group 2 innate lymphoid cell Double-positive, alpha-beta thymocyte Melanocyte Epithelial cell of nephron Smooth muscle cell Epithelial cell Skeletal muscle satellite cell Pre-conventional dendritic cell Plasmacytoid dendritic cell Enteroendocrine cell Early lymphoid progenitor Common dendritic progenitor Group 3 innate lymphoid cell Naive thymus-derived cd8-positive, alpha-beta t cell Macrophage Innate lymphoid cell Regulatory t cell Myelocyte Large pre-b-ii cell Mature b cell Promonocyte Keratinocyte Hematopoietic stem cell Glial cell Common myeloid progenitor Plasma cell Hematopoietic multipotent progenitor cell Megakaryocyte Langerhans cell Eurydendroid cell Mesothelial cell Cell of skeletal muscle Granulocyte monocyte progenitor cell Naive thymus-derived cd4-positive, alpha-beta t cell Promyelocyte Neuron Immature b cell Megakaryocyte-erythroid progenitor cell Fraction a pre-pro b cell Monocyte Vascular associated smooth muscle cell Myofibroblast cell Double negative thymocyte Fibroblast Osteoclast Dendritic cell Chondrocyte

Skin of body Thymus Yolk sac Liver Gut wall Kidney Spleen Bone marrow Mesenteric lymph node

Carnegie stage 19 13th week post-fertilization stage Carnegie stage 13 14th week post-fertilization stage 15th week post-fertilization stage 17th week post-fertilization stage 12th week post-fertilization stage 16th week post-fertilization stage Carnegie stage 20 9th week post-fertilization stage Carnegie stage 23 10th week post-fertilization stage Carnegie stage 22 11th week post-fertilization stage

Normal

Female Male

10x 3' v2 10x 5' v1

Cell

Homo sapiens

Neutrophil Club cell Cd1c-positive myeloid dendritic cell Stromal cell Natural killer cell Endothelial cell of lymphatic vessel Mast cell Cd8-positive, alpha-beta t cell Capillary endothelial cell Classical monocyte Smooth muscle cell Plasmacytoid dendritic cell Bronchus fibroblast of lung Macrophage Regulatory t cell Pulmonary alveolar type 1 cell Myeloid cell Fibroblast of lung Alveolar macrophage Plasma cell Cd4-positive, alpha-beta t cell Vein endothelial cell Malignant cell Mesothelial cell B cell Pericyte Pulmonary artery endothelial cell Epithelial cell of lung Multiciliated epithelial cell Conventional dendritic cell Dendritic cell Pulmonary alveolar type 2 cell Non-classical monocyte

Pleural effusion Lung Liver Brain Adrenal tissue Lymph node

66-year-old stage 69-year-old stage 37-year-old stage 75-year-old stage 21-year-old stage 65-year-old stage 42-year-old stage 26-year-old stage 43-year-old stage 71-year-old stage 53-year-old stage 61-year-old stage 52-year-old stage 54-year-old stage 68-year-old stage 48-year-old stage 29-year-old stage 56-year-old stage 55-year-old stage 82-year-old stage 50-year-old stage 80-year-old stage 28-year-old stage 51-year-old stage 57-year-old stage 72-year-old stage 74-year-old stage 49-year-old stage 23-year-old stage 35-year-old stage 58-year-old stage 59-year-old stage 25-year-old stage 67-year-old stage 32-year-old stage 77-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 78-year-old stage 31-year-old stage 36-year-old stage 22-year-old stage 63-year-old stage 20-year-old stage 47-year-old stage 76-year-old stage 79-year-old stage 73-year-old stage 83-year-old stage 40-year-old stage

Lung adenocarcinoma Chronic obstructive pulmonary disease Squamous cell lung carcinoma Normal Non-small cell lung carcinoma

Female Male

10x 3' v1 10x 3' v2 10x 3' v3 10x 5' v1 Bd rhapsody whole transcriptome analysis Drop-seq Gexscope technology Smart-seq2 Indrop

Cell

Homo sapiens

Central nervous system macrophage Oligodendrocyte precursor cell Endothelial cell Oligodendrocyte Committed oligodendrocyte precursor Ependymal cell Microglial cell Choroid plexus epithelial cell Bergmann glial cell Pericyte Vascular associated smooth muscle cell Astrocyte Fibroblast

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

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 Cell Endothelial cell Mast cell Epithelial cell Myeloid cell B cell Pericyte Fibroblast

Ovarian cancer Prostate cancer Clear cell renal carcinoma Liver cancer Colorectal carcinoma Pancreatic ductal adenocarcinoma Normal Breast carcinoma Lung cancer Urinary bladder cancer

10x technology 10x 3' v2 Visium spatial gene expression 10x 3' v3 Smart-seq2 10x 5' transcription profiling

Callithrix jacchus

Oligodendrocyte precursor cell Oligodendrocyte Ependymal cell Microglial cell Brain microvascular endothelial cell Mural cell Choroid plexus epithelial cell Neuron Astrocyte Fibroblast

Normal

10x 3' transcription profiling