Mus musculus

Granulosa cell Supporting cell Sertoli cell Ovarian surface epithelial cell Interstitial cell of ovary Mesenchymal cell Mesothelial cell Leydig cell

Mesonephros Gonad

Theiler stage 22 Theiler stage 27 Theiler stage 24 5-day-old stage Theiler stage 19 Theiler stage 26 Theiler stage 20 Theiler stage 21

Normal

Female Male

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

Cell

Homo sapiens

Neutrophil Blood vessel endothelial cell Natural killer cell Cd8-positive, alpha-beta t cell Cd4-positive helper t cell Peripheral nervous system neuron Schwann cell Macrophage Mural cell Odontoblast B cell Fibroblast Dendritic cell

Dental pulp

21-year-old stage 24-year-old stage 20-year-old stage Young adult stage

Normal

Female

10x 3' v3 10x 3' v2

Cell

Homo sapiens

Midbrain-derived inhibitory neuron T cell Central nervous system macrophage Natural killer cell Oligodendrocyte precursor cell Endothelial cell Oligodendrocyte Amygdala excitatory neuron Committed oligodendrocyte precursor Cerebellar granule cell Lamp5 lhx6 neuron Eccentric medium spiny neuron Medial ganglionic eminence derived interneuron Cerebellar inhibitory gabaergic interneuron Microglial cell Bergmann glial cell B cell Pericyte Cerebral cortex neuron Neuron Monocyte Intratelencephalic-projecting glutamatergic cortical neuron Caudal ganglionic eminence derived interneuron Vascular associated smooth muscle cell Sst chodl gabaergic interneuron Astrocyte Fibroblast Medium spiny neuron

Globus pallidus

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

Normal

Male

10x 3' v3

Nucleus

Homo sapiens

Dendritic cell, human Erythrocyte Mast cell Plasmacytoid dendritic cell, human Macrophage Trem2-positive macrophage Neutrophil progenitor cell Eosinophil Megakaryocyte Langerhans cell Monocyte Conventional dendritic cell

Ascending colon Colonic mucosa Stomach Duodenum Colonic epithelium Ileal epithelium Rectosigmoid junction Pyloric antrum Caecum Small intestine Gingiva Ileum Ileum lamina propria Lamina propria of mucosa of colon Colon Epithelium of rectum Epithelium of esophagus Intestine Buccal mucosa Body of stomach Vermiform appendix Epithelium of small intestine Pylorus Rectum Esophagus Jejunum Duodenal epithelium Transverse colon Periodontium Parotid gland Descending colon Sigmoid colon Labial gland Epithelium of stomach Mesenteric lymph node

66-year-old stage 69-year-old stage Carnegie stage 19 37-year-old stage 75-year-old stage Pediatric stage 19th week post-fertilization stage 21-year-old stage 13-year-old stage 21st week post-fertilization stage 34-year-old stage 65-year-old stage 26-year-old stage 43-year-old stage Sixth decade stage 87-year-old stage 13th week post-fertilization stage 85-year-old stage 61-year-old stage 2-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 56-year-old stage Fifth decade stage 55-year-old stage 84-year-old stage 15th week post-fertilization stage 50-year-old stage 80-year-old stage 28-year-old stage 51-year-old stage 17th week post-fertilization stage 57-year-old stage 12-year-old stage 72-year-old stage 12th week post-fertilization stage Third decade stage 16th week post-fertilization stage 81-year-old stage 9th week post-fertilization stage 74-year-old stage 9-year-old stage 10th week post-fertilization stage 14-year-old stage 24-year-old stage 23-year-old stage 35-year-old stage Seventh decade stage 58-year-old stage Embryonic stage 59-year-old stage Adult stage 67-year-old stage 18th week post-fertilization stage Carnegie stage 17 2-month-old stage 32-year-old stage 77-year-old stage 33-year-old stage Carnegie stage 22 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 31-year-old stage Fourth decade stage 22-year-old stage Newborn stage (0-28 days) 63-year-old stage Carnegie stage 16 Eighth decade stage 76-year-old stage Prime adult stage 5-year-old stage 11-year-old stage 6-year-old stage Young adult stage 10-year-old stage Carnegie stage 18 4-year-old stage 11th week post-fertilization stage Juvenile stage (5-14 yo)

Gastric cancer Inflammatory bowel disease Colorectal cancer Ulcerative colitis Normal Crohn disease

Female Male

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

Cell

Homo sapiens

T cell Central nervous system macrophage Natural killer cell Oligodendrocyte precursor cell Endothelial cell Oligodendrocyte Amygdala excitatory neuron Committed oligodendrocyte precursor Cerebellar granule cell Hippocampal ca1-3 neuron Lamp5 lhx6 neuron Eccentric medium spiny neuron Pvalb chandelier gabaergic interneuron Medial ganglionic eminence derived interneuron Microglial cell Pericyte Cerebral cortex neuron Neuron Intratelencephalic-projecting glutamatergic cortical neuron Caudal ganglionic eminence derived interneuron Vascular associated smooth muscle cell Sst chodl gabaergic interneuron Astrocyte Fibroblast Medium spiny neuron

Medial entorhinal cortex

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

Normal

Male

10x 3' v3

Nucleus

Homo sapiens

Periportal region hepatocyte Hepatocyte Centrilobular region hepatocyte Midzonal region hepatocyte

Caudate lobe of liver

Prime adult stage Young adult stage

Normal

Female Male

10x 3' v3 10x 3' v2

Cell Nucleus

Homo sapiens

Neutrophil Blood vessel endothelial cell Natural killer cell Endothelial cell of lymphatic vessel Cd8-positive, alpha-beta t cell Adult skeletal muscle myoblast Cd4-positive helper t cell Schwann cell Ionocyte Myoepithelial cell Macrophage Mural cell Keratinocyte Acinar cell of salivary gland Plasma cell Salivary gland glandular cell B cell Fibroblast Dendritic cell

Minor salivary gland Submandibular gland Parotid gland

69-year-old stage 34-year-old stage 26-year-old stage Sixth decade stage 53-year-old stage 48-year-old stage 39-year-old stage 56-year-old stage 28-year-old stage 24-year-old stage 59-year-old stage 62-year-old stage Fourth decade stage 40-year-old stage

Normal

Female Male

10x 3' v3

Cell

Mus musculus

Seminal vesicle glandular cell Luminal cell of prostate epithelium Urethra urothelial cell Basal cell of prostate epithelium

Prostate gland Urethra

2-month-old stage

Normal

Male

10x 3' v3 10x 3' v2

Cell

Mus musculus

T cell Endocardial cell Blood vessel endothelial cell Valve interstitial cell Endothelial cell of lymphatic vessel Mast cell Endothelial cell of artery Schwann cell Melanocyte Macrophage Valve endothelial cell Myocyte of sinoatrial node Mesothelial cell of epicardium B cell Pericyte Neuron Regular atrial cardiac myocyte Vascular associated smooth muscle cell Regular ventricular cardiac myocyte Fibroblast of cardiac tissue Chondrocyte

Heart

Theiler stage 22 Theiler stage 27 Theiler stage 24 Theiler stage 26 4-day-old stage 7-day-old stage

Normal

Female Male

Drop-seq

Cell

Danio rerio

Glutamatergic neuron Photoreceptor cell Neuroblast (sensu vertebrata) Glial cell Glycinergic neuron Gabaergic neuron Neural progenitor cell

Habenula Telencephalon Multicellular anatomical structure Zona limitans intrathalamica Brain Diencephalon Forebrain

Pharyngula:prim-15 Hatching:long-pec Larval:protruding-mouth Pharyngula:prim-25 Segmentation:26+ somites Segmentation:14-19 somites Hatching:pec-fin Segmentation:20-25 somites Pharyngula:high-pec Pharyngula:prim-5

Normal

Sci-rna-seq3

Nucleus

Homo sapiens

Midbrain-derived inhibitory neuron T cell Central nervous system macrophage Natural killer cell Oligodendrocyte precursor cell Endothelial cell Oligodendrocyte Committed oligodendrocyte precursor Cerebellar granule cell Cerebellar inhibitory gabaergic interneuron Ependymal cell Microglial cell Choroid plexus epithelial cell Bergmann glial cell B cell Pericyte Neuron Monocyte Intratelencephalic-projecting glutamatergic cortical neuron Caudal ganglionic eminence derived interneuron Purkinje cell Vascular associated smooth muscle cell Astrocyte Unipolar brush cell Fibroblast

Pontine reticular formation

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

Normal

Male

10x 3' v3

Nucleus

Homo sapiens

Glutamatergic neuron Oligodendrocyte precursor cell Endothelial cell Oligodendrocyte Vascular leptomeningeal cell Lamp5 gabaergic interneuron Microglial cell Vip gabaergic interneuron L2/3-6 intratelencephalic projecting glutamatergic neuron L5 extratelencephalic projecting glutamatergic cortical neuron L6b glutamatergic cortical neuron L6 corticothalamic-projecting glutamatergic cortical neuron Pvalb gabaergic interneuron Pericyte Near-projecting glutamatergic cortical neuron Caudal ganglionic eminence derived interneuron Astrocyte Sst gabaergic interneuron

Primary visual cortex Middle temporal gyrus Anterior cingulate gyrus Primary somatosensory cortex Primary auditory cortex Primary motor cortex

43-year-old stage 54-year-old stage 50-year-old stage

Normal

Female Male

Smart-seq v4

Nucleus