Mus musculus

Notochordal cell Spinal cord interneuron Paraxial cell Gut endothelial cell Splanchnic mesodermal cell Hemangioblast Cardiac valve cell Endodermal cell Primitive red blood cell Midbrain dopaminergic neuron Anterior visceral endoderm cell Premigratory neural crest cell Mesodermal cell Neuroplacodal cell Surface ectodermal cell

Embryo

Theiler stage 14

Normal

Slide-seqv2

Homo sapiens

Activated cd8-positive, alpha-beta t cell Naive thymus-derived cd4-positive, alpha-beta t cell Regulatory t cell B cell Cd4-positive, alpha-beta memory t cell Naive b cell Memory b cell Gamma-delta t cell Naive thymus-derived cd8-positive, alpha-beta t cell Cd16-negative, cd56-bright natural killer cell, human Activated cd4-positive, alpha-beta t cell Cd8-positive, alpha-beta memory t cell Mucosal invariant t cell Myeloid cell Cd16-positive, cd56-dim natural killer cell, human

Blood

26-year-old stage

Common variable immunodeficiency Normal

Male

10x 5' v1

Cell

Homo sapiens

Lymphocyte

Heart left ventricle Heart right ventricle Interventricular septum Apex of heart

Fourth decade stage Seventh decade stage Postnatal stage Fifth decade stage Pediatric stage Sixth decade stage Eighth decade stage Third decade stage

Dilated cardiomyopathy Arrhythmogenic right ventricular cardiomyopathy Normal Non-compaction cardiomyopathy

Female Male

10x 3' v2 10x 3' v3

Nucleus

Mus musculus

Kidney loop of henle thick ascending limb epithelial cell Kidney interstitial fibroblast Leukocyte Kidney proximal convoluted tubule epithelial cell Podocyte Kidney collecting duct principal cell Macrophage Blood vessel smooth muscle cell Endothelial cell Kidney collecting duct intercalated cell Mesangial cell Kidney granular cell Kidney distal convoluted tubule epithelial cell

Kidney

6-month-old stage

Autosomal dominant polycystic kidney disease

Male

Slide-seqv2

Mus musculus

Kidney loop of henle thick ascending limb epithelial cell Kidney interstitial fibroblast Leukocyte Kidney proximal convoluted tubule epithelial cell Podocyte Kidney collecting duct principal cell Macrophage Blood vessel smooth muscle cell Endothelial cell Kidney collecting duct intercalated cell Mesangial cell Kidney granular cell Kidney distal convoluted tubule epithelial cell

Kidney

13-week-old stage

Diabetic kidney disease

Male

Slide-seqv2

Mus musculus

Notochordal cell Spinal cord interneuron Paraxial cell Gut endothelial cell Splanchnic mesodermal cell Hemangioblast Cardiac valve cell Endodermal cell Primitive red blood cell Midbrain dopaminergic neuron Premigratory neural crest cell Mesodermal cell Neuroplacodal cell Surface ectodermal cell

Embryo

Theiler stage 14

Normal

Slide-seqv2

Homo sapiens

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

Hypothalamus

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

Normal

Male

10x 3' v3

Nucleus

Homo sapiens

Plasmacytoid dendritic cell Natural killer cell Dendritic cell Osteoblast Precursor b cell Regulatory t cell Progenitor cell Common myeloid progenitor Neutrophil Macrophage Cd8-positive, alpha-beta t cell Primitive red blood cell Erythrocyte Osteoclast Immature b cell Megakaryocyte Immature innate lymphoid cell Mature b cell Basophil mast progenitor cell Stromal cell Promyelocyte Cd16-negative, cd56-bright natural killer cell, human Endothelial cell Cd14-positive monocyte Mesenchymal stem cell Chondrocyte Promonocyte Hematopoietic multipotent progenitor cell Megakaryocyte-erythroid progenitor cell Mast cell Myelocyte Eosinophil

Bone marrow

Fourth lmp month stage 13th week post-fertilization stage 12th week post-fertilization stage

Down syndrome

Female Male

10x 5' v1

Cell

Homo sapiens

L2/3-6 intratelencephalic projecting glutamatergic neuron

Neocortex

Adult stage

Normal

Female Male

10x 3' v3

Cell

Homo sapiens

Natural killer cell Lymphocyte Cd4-positive, alpha-beta t cell Erythroblast Cd8-positive, alpha-beta t cell Mature b cell Hepatic pit cell Myeloid cell

Caudate lobe of liver

Young adult stage Prime adult stage Late adult stage

Normal

Female Male

10x 3' v2 10x 5' v1

Cell

Homo sapiens

Mammillary body neuron

Substantia nigra Dorsal tegmental nucleus Subthalamic nucleus Primary motor cortex Median tuberal portion Medial zone of hypothalamus Hypothalamus Intralaminar nuclear group Midbrain nucleus Medial geniculate body Mammillary body

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

Normal

Female Male

10x 3' v3

Nucleus

Danio rerio

Melanocyte Xanthoblast Melanoblast Xanthophore cell Iridophore

Multicellular anatomical structure Neural crest

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

Normal

Sci-rna-seq3

Nucleus