Homo sapiens

Central memory cd4-positive, alpha-beta t cell T cell Cd1c-positive myeloid dendritic cell Natural killer cell Double negative t regulatory cell Erythrocyte Gamma-delta t cell Cd8-positive, alpha-beta t cell Platelet Cd141-positive myeloid dendritic cell Effector memory cd4-positive, alpha-beta t cell Plasmacytoid dendritic cell Cd8-positive, alpha-beta memory t cell Cd4-positive, alpha-beta cytotoxic t cell Cd8-positive, alpha-beta cytotoxic t cell Naive thymus-derived cd8-positive, alpha-beta t cell Memory b cell Cd16-positive, cd56-dim natural killer cell, human Innate lymphoid cell Regulatory t cell Mature b cell Plasma cell Cd4-positive, alpha-beta t cell Cd14-positive monocyte Cd14-low, cd16-positive monocyte B cell Naive thymus-derived cd4-positive, alpha-beta t cell Mucosal invariant t cell Monocyte Naive b cell Conventional dendritic cell Dendritic cell Cd16-negative, cd56-bright natural killer cell, human

Blood

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 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 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 51-year-old stage 57-year-old stage 72-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 67-year-old stage 32-year-old stage 33-year-old stage 64-year-old stage 45-year-old stage 62-year-old stage 41-year-old stage 46-year-old stage 60-year-old stage 31-year-old stage 36-year-old stage 22-year-old stage 19-year-old stage 63-year-old stage 47-year-old stage 73-year-old stage 27-year-old stage 40-year-old stage

Normal

Female Male

10x 5' v2

Cell

Mus musculus

Erythroid 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

Oligodendrocyte precursor cell Endothelial cell Oligodendrocyte Cerebellar golgi cell Microglial cell Granule cell Interneuron Molecular layer interneuron Bergmann glial cell Pericyte Purkinje cell Astrocyte Unipolar brush cell

Essential tremor Normal

Parse evercode whole transcriptome v2

Homo sapiens

Visceromotor neuron Ganglion interneuron Endocardial cell Bipolar neuron Blood vessel endothelial cell Stromal cell Endothelial cell of lymphatic vessel Glutamatergic neuron Chorionic trophoblast cell Oligodendrocyte Chromaffin cell Neuroendocrine cell Retinal ganglion cell Retinal pigment epithelial cell Stellate neuron Corneal epithelial cell Hepatoblast Trophoblast giant cell Enteric neuron Extravillous trophoblast Sympathetic neuron Cortical cell of adrenal gland Schwann cell Taste receptor cell Smooth muscle cell Skeletal muscle satellite cell Inhibitory interneuron Hepatic stellate cell Endothelial cell of vascular tree Goblet cell Thymocyte Photoreceptor cell Tuft cell Endocrine cell Microglial cell Granule cell Neuron associated cell (sensu vertebrata) Innate lymphoid cell Dermis microvascular lymphatic vessel endothelial cell Myeloid cell Ventricular cardiac muscle cell Hematopoietic stem cell Glial cell Intestinal epithelial cell Retina horizontal cell Mesangial cell Megakaryocyte Squamous epithelial cell Amacrine cell Acinar cell Mesothelial cell Cell of skeletal muscle Epithelial cell of lower respiratory tract Ciliated epithelial cell Cardiac muscle cell Macroglial cell Lens fiber cell Professional antigen presenting cell Mueller cell Epicardial adipocyte Neuron Regular atrial cardiac myocyte Purkinje cell Pancreatic ductal cell Syncytiotrophoblast cell Erythroblast Astrocyte Unipolar brush cell Epithelial cell of thymus Gabaergic neuron Hematopoietic cell

Adrenal gland Cerebellum Eye Heart Intestine Kidney Liver Lung Muscle organ Pancreas Placenta Spleen Stomach Telencephalon Thymus

13th week post-fertilization stage 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 10th week post-fertilization stage 18th week post-fertilization stage

Normal Trisomy 18

Female Male

Sci-rna-seq3

Nucleus 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

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

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

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

Nucleus Cell

Homo sapiens

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

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

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

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

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

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

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 5' v1 10x 3' v2

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

Adrenal tissue Brain Liver Lung Lymph node Pleural effusion

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

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

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

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