Homo sapiens

Central memory cd4-positive, alpha-beta t cell Natural killer cell Gamma-delta t cell Effector memory cd4-positive, alpha-beta t cell Classical monocyte Myeloid dendritic cell Cd8-positive, alpha-beta memory t cell Naive thymus-derived cd8-positive, alpha-beta t cell Effector memory cd8-positive, alpha-beta t cell, terminally differentiated Memory b cell Plasmablast Cd4-positive, alpha-beta t cell Naive thymus-derived cd4-positive, alpha-beta t cell Naive b cell Non-classical monocyte

Blood

Middle aged stage Adult stage 60-79 year-old stage Young adult stage

Rheumatoid arthritis Normal

Female Male

10x 3' v3

Cell

Mus musculus

Primitive erythroid progenitor

Embryo

Theiler stage 22 Theiler stage 27 Theiler stage 24 Theiler stage 18 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

T cell Neutrophil Stromal cell Natural killer cell Pulmonary capillary endothelial cell Lung multiciliated epithelial cell Lung macrophage Pulmonary alveolar type 1 cell Vein endothelial cell B cell Pulmonary artery endothelial cell Monocyte

Lingula of left lung Upper lobe of left lung Lower lobe of right lung Middle lobe of right lung Upper lobe of right lung

66-year-old stage 37-year-old stage 65-year-old stage 43-year-old stage 71-year-old stage 55-year-old stage 28-year-old stage 51-year-old stage 64-year-old stage 36-year-old stage 19-year-old stage

Normal

Female Male

10x 3' v3

Cell

Homo sapiens

Skin fibroblast

Skin of abdomen Skin of back Skin of body Skin of trunk Skin of leg Lower leg skin Skin of cheek Skin of shoulder Skin of forearm Skin of face Inguinal region skin Skin of hip Skin of chest Skin of pes Hindlimb skin

66-year-old stage 37-year-old stage 75-year-old stage 34-year-old stage 65-year-old stage 42-year-old stage 26-year-old stage 43-year-old stage 53-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 28-year-old stage 51-year-old stage 57-year-old stage 74-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 62-year-old stage 41-year-old stage 46-year-old stage 18-year-old stage 31-year-old stage 36-year-old stage 22-year-old stage 63-year-old stage 47-year-old stage 79-year-old stage 73-year-old stage 27-year-old stage

Localized scleroderma Normal Keloid Injury

Female Male

10x 3' v1 10x 5' v1 10x 3' v3 10x 3' v2 Mars-seq Seq-well s3

Cell

Mus musculus

L2/3 intratelencephalic projecting glutamatergic neuron L5/6 near-projecting glutamatergic neuron Oligodendrocyte precursor cell L5 intratelencephalic projecting glutamatergic neuron L4/5 intratelencephalic projecting glutamatergic neuron Endothelial cell Oligodendrocyte Vascular leptomeningeal cell Lamp5 gabaergic interneuron Microglial cell Vip gabaergic interneuron L5 extratelencephalic projecting glutamatergic cortical neuron L6b glutamatergic cortical neuron L6 corticothalamic-projecting glutamatergic cortical neuron Pvalb gabaergic interneuron Pericyte Perivascular macrophage L6 intratelencephalic projecting glutamatergic neuron Sncg gabaergic interneuron Astrocyte Sst gabaergic interneuron

Cerebral cortex

Prime adult stage

Normal

Male

10x 3' v3

Nucleus

Homo sapiens

Basal cell Epithelial cell Glandular cell of esophagus Keratinocyte Cycling basal cell

Epithelium of esophagus Esophagus

Sixth decade stage Fifth decade stage 15th week post-fertilization stage 17th week post-fertilization stage Seventh decade stage 31-year-old stage Fourth decade stage

Normal

Female Male

10x 5' transcription profiling 10x 3' v2

Cell

Homo sapiens

T cell Germinal center b cell Igm plasma cell Natural killer cell Endothelial cell of lymphatic vessel Follicular dendritic cell Secretory cell Endothelial cell Mast cell Iga plasma cell Endothelial cell of artery Capillary endothelial cell Paneth cell Epithelial cell Plasmacytoid dendritic cell Igg plasma cell Enteroendocrine cell Goblet cell Macrophage Innate lymphoid cell Mural cell Myeloid cell Glial cell Vein endothelial cell Transit amplifying cell B cell Monocyte Myofibroblast cell Epithelial fate stem cell Fibroblast Dendritic cell M cell of gut

Crohn's colitis

10x 3' v2

Homo sapiens

T cell Podocyte Natural killer cell Parietal epithelial cell Kidney interstitial alternatively activated macrophage Cytotoxic t cell Endothelial cell Kidney loop of henle thin descending limb epithelial cell Mature nk t cell Mast cell Kidney collecting duct intercalated cell Epithelial cell of proximal tubule Plasmacytoid dendritic cell, human Kidney distal convoluted tubule epithelial cell Kidney collecting duct principal cell Kidney connecting tubule epithelial cell Regulatory t cell Kidney loop of henle thick ascending limb epithelial cell Kidney interstitial cell Plasma cell B cell Monocyte Kidney loop of henle thin ascending limb epithelial cell Conventional dendritic cell Non-classical monocyte Mononuclear phagocyte

Kidney

66-year-old stage 42-year-old stage Sixth decade stage 53-year-old stage 52-year-old stage 48-year-old stage 30-year-old stage 39-year-old stage 56-year-old stage Fifth decade stage 57-year-old stage Third decade stage 49-year-old stage 35-year-old stage Seventh decade stage 41-year-old stage 31-year-old stage Fourth decade stage Eighth decade stage 47-year-old stage 40-year-old stage

Chronic kidney disease Normal Acute kidney failure

Female Male

10x 3' v3

Cell

Homo sapiens

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

Middle temporal gyrus

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

Normal

Male

10x 3' v3

Nucleus

Mus musculus

T cell Neutrophil Oligodendrocyte precursor cell Endothelial cell Oligodendrocyte Ependymal cell Macrophage Microglial cell Choroid plexus epithelial cell B cell Pericyte Neuron Myeloid leukocyte Astrocyte Fibroblast Neural progenitor cell

Brain ischemia Normal

10x 3' v2

Homo sapiens

T cell Neutrophil Merkel cell Endothelial cell of venule Natural killer cell Endothelial cell of lymphatic vessel Gamma-delta t cell Mature nk t cell Mast cell Endothelial cell of artery Capillary endothelial cell Schwann cell Melanocyte Plasmacytoid dendritic cell T-helper 17 cell Macrophage Regulatory t cell Helper t cell Keratinocyte Plasma cell Langerhans cell B cell Pericyte Mucosal invariant t cell Vascular associated smooth muscle cell Conventional dendritic cell Fibroblast

Gingiva

37-year-old stage 21-year-old stage 34-year-old stage 42-year-old stage 26-year-old stage 61-year-old stage 30-year-old stage 39-year-old stage 44-year-old stage 29-year-old stage 38-year-old stage 28-year-old stage 51-year-old stage 57-year-old stage 24-year-old stage 35-year-old stage Adult stage 32-year-old stage 45-year-old stage 31-year-old stage 22-year-old stage Young adult stage

Gingivitis Periodontitis Normal

Female Male

10x 3' v3 10x 3' v2

Cell

Homo sapiens

Effector cd8-positive, alpha-beta t cell Gamma-delta t cell Plasmacytoid dendritic cell Effector cd4-positive, alpha-beta t cell Cd8-positive, alpha-beta memory t cell Naive thymus-derived cd8-positive, alpha-beta t cell Cd4-positive, cd25-positive, alpha-beta regulatory t cell Memory b cell Cd16-positive, cd56-dim natural killer cell, human Plasmablast Cd14-low, cd16-positive monocyte Naive thymus-derived cd4-positive, alpha-beta t cell Cd14-positive, cd16-negative classical monocyte Naive b cell Conventional dendritic cell Cd16-negative, cd56-bright natural killer cell, human

Blood

13-year-old stage 2-year-old stage 17-year-old stage 8-year-old stage 15-year-old stage 9-year-old stage 14-year-old stage 16-year-old stage 3-year-old stage 18-year-old stage 1-year-old stage 5-year-old stage 11-year-old stage 7-year-old stage 4-year-old stage

Juvenile dermatomyositis Normal

Female Male

10x 3' v3

Cell