Journal: bioRxiv

Article Title: Investigation of cell mechanics and migration on DDR2-expressing neuroblastoma cell line

doi: 10.1101/2024.08.15.607761

Figure Lengend Snippet: A) DDR2 mRNA expression across cancer lines was analyzed in the Dependency Map Portal ( https://depmap.org/portal ; Broad Institute). B) Western blot of DDR2 expression (vs. GAPDH) upon 4 days of doxycycline treatment (0-12.5 mg/mL) on Tet-shDDR2 SHSY5Y cells. C) Cell survival/proliferation time course assay (as measured by % confluency) of Tet-shDDR2 SHSY5Y cells treated with doxycycline (on day 0) at increasing concentrations as indicated (n = 6 wells/condition). D) Western blot of DDR2 and phospho-Tyrosine 720-DDR2 (phY720-DDR2) from Tet-shDDR2 SHSY5Y cells pretreated for 3 days with the indicated concentrations of doxycycline and left unstimulated or induced with 25 mg/mL of rat tail Type I collagen for 16 hours.

Article Snippet: Primary antibodies were: from Cell Signaling Technology DDR2 (#12133); from MilliporeSigma Anti-GAPDH antibody (MAB374); and from R&D Systems human phopho-DDR1/DDR2 (Y796/Y740) antibody (MAB25382).

Techniques: Expressing, Western Blot

Journal: Theranostics

Article Title: Fibroblasts facilitate lymphatic vessel formation in transplanted heart

doi: 10.7150/thno.92103

Figure Lengend Snippet: Fibroblasts Display Activated Phenotype in Allograft Heart. A , t-SNE plot of fibroblast populations of control group ( BALB/c ) and allograft-2 w group. Cd34.high.FB, high expression of FB; ECM.FB, enriched genes and functions related to ECM organization; JF.high.FB, high expression of Jun and Fos ; IFN.FB, high expression of genes related to interferon. B , Pie plot showing the percentage of cell composition in two groups (inside: control; outside: allo-2 w). C , Dot plot shows selected GO terms enriched in fibroblast sub-clusters. D , Violin plot showing the combination expression level (right) of selected activated fibroblast genes (left) in sub-population from two groups. E , Bar plot showing the percentage of activated fibroblasts and other fibroblasts in two datasets. The activated fibroblasts were identified according to combination expression level of genes in Figure d. F , Ridgeline chart showing the expression score of fibrosis-related score in fibroblasts from two groups. G , mRNA quantification of activated fibroblast-associated genes in the hearts from two groups, mRNA expression in the control group as the criterion (1.0). Number of mice in each group: n = 9 (Control), n = 6 (Allo-2 w); unpaired t-test. Postn (Periostin), Col1a1 (Collagen, type I, alpha 1), Col3a1 (Collagen, type III, alpha 1), Ddr2 (Discoidin domain-containing receptor 2), Fn1 (Fibronectin), Pdgfra (Platelet-derived growth factor receptorα). H , I , Immunostaining ( H ) and quantification ( I ) of POSTN expression in control group and allograft group, the area of POSTN expression in the control group as the criterion (1.0). The images within the dashed box are displayed in the second row. Number of mice in each group: n = 4 (Control), n = 4 (Allo-1 w), n = 7 (Allo-2 w); one-way ANOVA test. J , Immuno-staining of POSTN and LYVE1, Collagen I and LYVE1, DDR2 and LYVE1 in two groups. The images within the dashed box are displayed in the second row. Scale bars, 100 µm (H,J). Allo: allograft; FB: fibroblast.

Article Snippet: Primary antibodies were applied in this study as listed: LYVE1 (abcam, ab14917, 1:300), VEGFR3 (R&D Systems, AF349, 1:50), tdTomato (Rockland, 600-401-379, 1:500), Periostin (R&D system, AF2955, 1:50), Collagen Type I (Proteintech, 67288-1-Ig, 1:100 ), DDR2 (discoidin domain receptor 2, R&D Systems, MAB25381, 1:100), PDGFRα (R&D Systems, AF1062, 1:50), PCNA (Abclonal, A0264, 1:500), KI67 (abcam, ab16667, 1:500), VEGFD (Proteintech, 26915-1-AP, 1:50), Midkine (Proteintech, 11009-1-AP, 1:50), SEMA3C (R&D Systems,MAB1728, 1:50), PTN (abcam, ab79411, 1:50), NRP2 (Neuropilin-2, CST, D39A5, 1:50), NCL (nucleolin, Santa cruz, sc-8031, 1:50), Vimentin (abcam, ab8978, 1:100), Fibronectin (abcam, ab2413, 1:50), CD31 (R&D, AF3628, 1:50), CD31 (abcam, ab28364, 1:50), SMA-FITC (Sigma, F3777, 1:300), p-AKT(Santa cruz, sc-514032, 1:50), p-ERK (Santa cruz, sc-7383, 1:50), CD45 (R&D Systems, AF114, 1:50), TNF-α(Proteintech, 60291-1-Ig, 1:50), IL1β (Abclonal, a19635, 1:50), IL6 (Proteintech, 66146-1-Ig, 1:50).

Techniques: Control, Expressing, Derivative Assay, Immunostaining