Journal: iScience

Article Title: Patterning the embryonic pulmonary mesenchyme

doi: 10.1016/j.isci.2022.103838

Figure Lengend Snippet: Computationally identified mesenchymal clusters represent spatially distinct populations (A) Violin plots showing the expression of Hoxb6 or Ptn in each cluster. (B) Fluorescence in situ hybridization for Hoxb6 and Ptn in E 11.5 lungs. Scale bar shows 25 μm. (C) Violin plots showing the expression of Lef1 or Foxp1 in each cluster. (D) E 11.5 lungs immunostained for cluster 0 marker Lef1 or for cluster 1 marker Foxp1 and counterstained with Hoechst. Scale bars show 25 μm. (E) Quantifications of Lef1 and Foxp1 intensity profiles emanating from the epithelium (for Lef1) or from the mesothelium (for Foxp1). Schematics show lines and direction along which intensity profiles were measured. Mean and SD are plotted (n = 4). (F) Schematic depicting the sub-epithelial and sub-mesothelial compartments of the mesenchyme. (G) Heatmap showing the expression of genes specific to either mesenchymal compartment. Genes (rows) are clustered based on the dendrogram to the right. Cells (columns) are clustered based on the dendrogram above, and each column is color-coded according to the original cluster identity from Figure 1 B. (H) UMAP of mesenchymal and smooth muscle cells color-coded according to the sum of their expression of either sub-epithelial or sub-mesothelial mesenchyme marker genes. Dotted line indicates the location of smooth muscle cells

Article Snippet: Rabbit polyclonal Foxp1 antibody , Cell Signaling , Cat# 2005; RRID: AB_2106979.

Techniques: Expressing, Fluorescence, In Situ Hybridization, Marker

Journal: iScience

Article Title: Patterning the embryonic pulmonary mesenchyme

doi: 10.1016/j.isci.2022.103838

Figure Lengend Snippet: Wnt signaling regulates cell identity in the embryonic pulmonary mesenchyme. (A) Bubble plot showing the enrichment percentage and adjusted p value of relevant GO terms identified based on genes upregulated in each mesenchymal cluster. (B) Heatmap showing the expression of Wnt-associated genes upregulated in either mesenchymal cluster. Activators and targets are colored in blue, inhibitors are colored in red. (C) Heatmap showing the expression of Wnt ligands, secreted inhibitors, and receptors detected in either mesenchymal cluster and in clusters containing cells from the mesothelium (meso), vascular endothelium (ve), epithelium (ep), and smooth muscle (sm). (D–G) Confocal sections and quantification of Lef1 and Foxp1 intensity profiles around branch L.L2 in lungs isolated at E 11.5 from CD1 embryos and immunostained for Lef1 or Foxp1 after treatment with either DMSO, LiCl (10 mM), or IWR1 (100 μM) for 24 h (n = 2–6). Yellow dashed lines indicate the border of the epithelium. Schematics show lines and direction along which intensity profiles were measured. Mean and SEM are plotted, and curves were compared using two-way ANOVA. (H–M) E 12.5 control and Tbx4-rtTA ; tet-O-Cre ; Ctnnb1 fl/fl lungs immunostained for Lef1 or Foxp1 and quantification of Lef1 and Foxp1 intensity profiles (n = 3). Low-magnification z-projections (H and I) and high-magnification confocal slices (J and K) are shown. Scale bars show 50 μm. ∗ indicates p<0.05, ∗∗ indicates p<0.001, and ∗∗∗ indicates p<0.0001

Article Snippet: Rabbit polyclonal Foxp1 antibody , Cell Signaling , Cat# 2005; RRID: AB_2106979.

Techniques: Expressing, Isolation, Control

Journal: iScience

Article Title: Patterning the embryonic pulmonary mesenchyme

doi: 10.1016/j.isci.2022.103838

Figure Lengend Snippet: Regulators and features of smooth muscle differentiation (A) Sections of E 12.5 Dermo1-Cre/+; Yap fl/fl ; mTmG/+ lungs and littermate controls immunostained for GFP and either Yap1, Lef1, Foxp1, or αSMA. Insets show zoomed-in view of the mesenchyme to highlight the decrease in mesenchymal Yap1 levels in mutants. Yap1 + cells in the mesenchyme of mutants are vascular endothelial cells (ve, indicated by white arrowheads), which are not targeted by Dermo1-Cre . ep is epithelium. Scale bars show 50 μm. (B) Scaled expression of genes involved in cytoskeleton, cell adhesion, and extracellular matrix versus cell loadings along DC1 compared to the expression profiles of the smooth muscle markers Acta2 and Myocd (dotted lines). Pearson correlation coefficients and significance are indicated and lines represent smoothed data with SE shaded in gray. (C) Simplified pathway diagram depicting the steps of proliferative metabolism and showing relevant enzymes at each step. Enzymes that are significantly downregulated along DC1 are indicated in bold red font, with a significance of spline fit indicated by asterisks. ∗ indicates p < 0.05, ∗∗ indicates p < 0.001, and ∗∗∗ indicates p < 0.0001

Article Snippet: Rabbit polyclonal Foxp1 antibody , Cell Signaling , Cat# 2005; RRID: AB_2106979.

Techniques: Expressing

Journal: iScience

Article Title: Patterning the embryonic pulmonary mesenchyme

doi: 10.1016/j.isci.2022.103838

Figure Lengend Snippet:

Article Snippet: Rabbit polyclonal Foxp1 antibody , Cell Signaling , Cat# 2005; RRID: AB_2106979.

Techniques: Recombinant, RNAscope, Multiplex Assay, Mutagenesis, Software, Sequencing

Journal: Cell

Article Title: Food Perception Primes Hepatic ER Homeostasis via Melanocortin-Dependent Control of mTOR Activation

doi: 10.1016/j.cell.2018.10.015

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: p-S6 ribosomal protein antibody , Cell Signaling , Cat# 2215S; RRID: AB_331682.

Techniques: Virus, Plasmid Preparation, Recombinant, Western Blot, Electron Microscopy, Clinical Proteomics, Modification, Enzyme-linked Immunosorbent Assay, Reverse Transcription, BIA-KA, RNAscope, Multiplex Assay, Fluorescence, Sample Prep, Software

Journal: Cell

Article Title: Food Perception Primes Hepatic ER Homeostasis via Melanocortin-Dependent Control of mTOR Activation

doi: 10.1016/j.cell.2018.10.015

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: p-p70 S6 kinase antibody , Cell Signaling , Cat# 9234; RRID: AB_2269803.

Techniques: Virus, Plasmid Preparation, Recombinant, Western Blot, Electron Microscopy, Clinical Proteomics, Modification, Enzyme-linked Immunosorbent Assay, Reverse Transcription, BIA-KA, RNAscope, Multiplex Assay, Fluorescence, Sample Prep, Software

Journal: Neuron

Article Title: Driving axon regeneration by orchestrating neuronal and non-neuronal innate immune responses via the IFNγ-cGAS-STING axis

doi: 10.1016/j.neuron.2022.10.028

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Rabbit anti-S100β , Cell Signaling , Cat#9550; RRID: AB_10949319.

Techniques: Control, Virus, Plasmid Preparation, Recombinant, RNAscope, Multiplex Assay, Fluorescence, Reverse Transcription, SYBR Green Assay, Single Cell Gel Electrophoresis, Knock-Out, Knock-In, shRNA, Sequencing, Software

Journal: Developmental cell

Article Title: Specialized endothelial tip cells guide neuroretina vascularization and blood-retina-barrier formation

doi: 10.1016/j.devcel.2021.06.021

Figure Lengend Snippet: (A) Experimental strategy to delete Smad2 and Smad3 in ECs. Red arrows indicate TAM injections. (B and C) Western blot for SMAD2 or SMAD3 and β-actin using ECs isolated from lungs of WT ( Smad2l/l or Smad3l/l ) and Smad2iEKO and Smad3iEKO mice, respectively. (D) IsoB4/α-SMA double staining of P12 retinas of the indicated genotypes. (E) Quantification of vascular parameters of Smad2/3l/l and Smad2/3iEKO P12 retinas (mean ± SEM, each dot represents one retina, *p < 0.05, **p < 0.01, Mann-Whitney U test). (F) Experimental strategy to delete Smad4 in ECs. Red arrows indicate TAM injections. (G) IsoB4 and α-SMA double staining of P12 Smad4l/l and Smad4iEKO retinas. (H) Quantification of vascular parameters of P12 retinas of the indicated genotypes (mean ± SEM, each dot represents one retina, *p < 0.05, **p < 0.01, **p < 0.001, Mann-Whitney U test). (I) Double immunostainings for IsoB4 and APOE, VWF, TXNDR1, or PLVAP of retina flat mounts of the indicated genotypes at P12. A, artery; V, vein.

Article Snippet: Rabbit Anti-Smad3 (C67H9) monoclonal antibody , Cell Signaling , Cat#9523; RRID: AB_2193182.

Techniques: Western Blot, Isolation, Double Staining, MANN-WHITNEY

Journal: Developmental cell

Article Title: Specialized endothelial tip cells guide neuroretina vascularization and blood-retina-barrier formation

doi: 10.1016/j.devcel.2021.06.021

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Rabbit Anti-Smad3 (C67H9) monoclonal antibody , Cell Signaling , Cat#9523; RRID: AB_2193182.

Techniques: Recombinant, Saline, Fluorescence, Plasmid Preparation, Modification, Western Blot, cDNA Synthesis, SYBR Green Assay, Imaging, RNAscope, Multiplex Assay, Gene Expression, Software, Laser-Scanning Microscopy