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 Hippocampal ca1-3 neuron Lamp5 lhx6 neuron Pvalb chandelier gabaergic interneuron Medial ganglionic eminence derived interneuron Ependymal cell Microglial cell Thalamic excitatory neuron Choroid plexus epithelial cell Pericyte Near-projecting glutamatergic cortical neuron Neuron Monocyte Intratelencephalic-projecting glutamatergic cortical neuron Caudal ganglionic eminence derived interneuron Sst chodl gabaergic interneuron Astrocyte Fibroblast Mammillary body neuron

Hypothalamus

42-year-old stage

Normal

Male

10x 3' v3

Nucleus

Mus musculus

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

Embryo

Theiler stage 14

Normal

Slide-seqv2

Mus musculus

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

Kidney

13-week-old stage

Normal

Male

Slide-seqv2

Mus musculus

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

Kidney

13-week-old stage

Diabetic kidney disease

Male

Slide-seqv2

Homo sapiens

Cortical thymic epithelial cell Medullary thymic epithelial cell Epithelial cell of thymus

Thymus

13th week post-fertilization stage 3-month-old stage 15th week post-fertilization stage 17th week post-fertilization stage 12th week post-fertilization stage 16th week post-fertilization stage 9th week post-fertilization stage 10th week post-fertilization stage Organogenesis stage 15-19 year-old Fourth decade stage 11th week post-fertilization stage

Normal

Female Male

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

Cell

Homo sapiens

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

Renal medulla

54-year-old stage

Normal

Male

Slide-seqv2

Homo sapiens

Corticothalamic-projecting glutamatergic cortical neuron

Middle temporal gyrus

69-year-old stage 75-year-old stage 65-year-old stage 89-year-old stage 43-year-old stage 87-year-old stage 85-year-old stage 88-year-old stage 68-year-old stage 29-year-old stage 84-year-old stage 82-year-old stage 50-year-old stage 80-year-old stage 72-year-old stage 81-year-old stage 80 year-old and over stage Adult stage 77-year-old stage 86-year-old stage 70-year-old stage 60-year-old stage 78-year-old stage 83-year-old stage

Normal Dementia

Female Male

10x multiome 10x 3' v3

Nucleus

Homo sapiens

Ciliated cell Endothelial cell of lymphatic vessel Endothelial cell Smooth muscle cell Pulmonary alveolar type 1 cell Epithelial cell of lower respiratory tract Pericyte Fibroblast Pulmonary alveolar type 2 cell

Alveolus of lung

65-year-old stage 61-year-old stage 60-year-old stage 63-year-old stage 73-year-old stage

Pulmonary emphysema Normal

Female Male

10x 3' v3

Cell

Homo sapiens

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

Renal medulla

64-year-old stage

Normal

Female

Slide-seqv2

Homo sapiens

Stromal cell Endothelial cell Leukocyte Smooth muscle cell Pericyte

Ovary

65-year-old stage 58-year-old stage 62-year-old stage

Normal

Female

10x scatac-seq

Nucleus

Mus musculus

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

Embryo

Theiler stage 14

Normal

Slide-seqv2

Mus musculus

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

Kidney

6-month-old stage

Autosomal dominant polycystic kidney disease

Male

Slide-seqv2