Journal: iScience

Article Title: Combined metabolomic and transcriptomic profiling approaches reveal the cardiac response to high-fat diet

doi: 10.1016/j.isci.2022.104184

Figure Lengend Snippet:

Article Snippet: Plasmid: pCMV Flag ERR1 , Addgene , #10975.

Techniques: Marker, Extraction, Transfection, Lysis, Luciferase, Protease Inhibitor, RNA Sequencing, Recombinant, Plasmid Preparation, Software

Journal: Cell stem cell

Article Title: Neutralizing Gatad2a-Chd4-Mbd3/NuRD Complex Facilitates Deterministic Induction of Naïve Pluripotency

doi: 10.1016/j.stem.2018.07.004

Figure Lengend Snippet: List of RT-PCR primers used in this study.

Article Snippet: DNA plasmids DNA plasmids used in this study for ectopic expression included: Fuw-Flag-Mbd3 (Addgene 52371), FUW-Flag-Mbd3 delta1-70 (Addgene 52372), FUW-2XFlag-ΔCCR-Mbd3 (Deletion of 220-279), FUW-Gatad2a, FUW-Gatad2b, pCAG-HA-Gatad2a-CCR (140-174 of Gatad2a), pCAG-HA-(MBD)Mbd3 (1-170 of Mbd3), pCAG-HA-GFP, FUW-Gatad2a-mutatnt ((K30R, K485R) SUMOylation-sites).

Techniques: Recombinant, Protease Inhibitor, Sample Prep, Methylation, Knock-In, Negative Control, Reverse Transcription Polymerase Chain Reaction, Software

Journal: Science advances

Article Title: BRD9 functions as a methylarginine reader to regulate AKT-EZH2 signaling.

doi: 10.1126/sciadv.ads6385

Figure Lengend Snippet: Fig. 5. BRD9 regulates H3K27me3 levels through the AKT1-EZH2 axis. (A) IB analysis of WCL derived from MDA-MB-231 cells infected with lentivirus of sgGFP or sg- BRD9. (B) IB analysis of WCL derived from MDA-MB-231 cells treated with indicated doses of dBRD9 for 16 hours. (C) IB analysis of WCL derived from MDA-MB-231 cells infected with lentivirus of sgGFP or sgBRD9. Cells were treated with 5 μM GSK126 for 16 hours before harvesting. (D) IB analysis of WCL derived from MDA-MB-231 cells treated with indicated doses of I-BRD9 for 16 hours. (E) IB analysis of WCL derived from MDA-MB-231 cells stably expressing EV or Myr-AKT1 and depleted of BRD9 in- fected with lentivirus sgGFP (−) or sgBRD9 (+). (F) IB analysis of WCL derived from control (sgGFP) or AKT1-depleted MDA-MB-231 cells. Cells were treated with 5 μM I- BRD9 for 16 hours before harvesting. (G) RT-qPCR analysis of mRNA levels of select genes in MDA-MB-231 cells treated with DMSO or 5 μM GSK126 for 48 hours. Data are shown as means ± SD of n = 3 biological replicates. *P < 0.05, **P < 0.01, and ***P < 0.001, Student’s t test.

Article Snippet: Myr- AKT1 (64606) and HA- EZH2 (173717) were purchased from Addgene.

Techniques: Derivative Assay, Infection, Stable Transfection, Expressing, Control, Quantitative RT-PCR

Journal: Science advances

Article Title: BRD9 functions as a methylarginine reader to regulate AKT-EZH2 signaling.

doi: 10.1126/sciadv.ads6385

Figure Lengend Snippet: Fig. 6. Combined treatment of BRD9 and EZH2 inhibitors leads to synergistic growth inhibition of breast cancer. (A) Inhibition of cell viability and dose-response matrixes analyzed by SynergyFinder. MDA-MB-231 cells were treated with the indicated doses of I-BRD9 and GSK126 for 96 hours prior to analysis of cell viability. (B) MDA- MB-231 cells treated with I-BRD9 or GSK126 were subjected to cell proliferation assays. Data are shown as means ± SD of n = 3 biological replicates. ***P < 0.001, two-way ANOVA and Tukey post hoc test. (C) MDA-MB-231 cells treated with I-BRD9 or GSK126 were subjected to colony formation assays. Representative images are shown. (D) Quantification of colonies in (C). Data are shown as means ± SD of n = 3 biological replicates. *P < 0.05 and ***P < 0.001, one-way ANOVA and Tukey post hoc test. (E) Schematic of a mouse xenograft assay to evaluate the antitumor effects of I-BRD9 and GSK126. (F) Tumor growth curve upon treatment of I-BRD9 and GSK126. Data are shown as means ± SEM of n = 6 mice for each group. *P < 0.05, two-way ANOVA and Tukey post hoc test. (G and H) Dissected tumors were weighed. Data are shown as the means ± SEM of n = 6 tumors for each group. *P < 0.05, one-way ANOVA and Tukey post hoc test. (I) Representative images of TUNEL assays in xenograft tumors in (G). (J) Schematic depicting the function of the BRD9-AKT-EZH2 axis in regulating transcription and tumor growth.

Article Snippet: Myr- AKT1 (64606) and HA- EZH2 (173717) were purchased from Addgene.

Techniques: Inhibition, Xenograft Assay, TUNEL Assay

Journal: bioRxiv

Article Title: Manganese mediates antiviral effects by driving an ATM-TBK1 phosphorylation signaling pathway

doi: 10.1101/2025.08.20.671272

Figure Lengend Snippet: (A) A549 wild-type and ATM KO A549 cells were treated with increasing concentrations of MnCL 2 . Total cell lysates were collected 24 hours post-treatment using RIPA buffer and analyzed by Western blot using antibodies against ATM, TBK1, and p-TBK1. β-actin served as a loading control. (B) A549 and ATM KO A549 cells were treated with the indicated concentrations of MnCL 2 , followed by stimulation with linearized DNA 24 hours later. After an additional 24 hours, total RNA was extracted, and IFN-λ1 mRNA expression levels were measured by quantitative RT-PCR and normalized to GAPDH. (C–F) 293T cells ( C ), HeLa cells ( D ), MDMs ( E ), and PHA-activated CD4⁺ T cells ( F ) were treated with varying doses of MnCL 2 . Whole cell lysates were collected after 24 hours and analyzed by Western blot using anti-ATM, anti-p-TBK1, and anti-TBK1 antibodies. β-actin was included as an internal loading control.

Article Snippet: The plasmids pcDNA3.1(+) Flag-His-ATM wild-type (wt), pcDNA3.1(+) Flag-His-ATM kinase-dead (kd), and hATM-S1981A (Addgene, Watertown, MA, USA) were used to overexpress either wild-type or mutant forms of ATM.

Techniques: Western Blot, Control, Expressing, Quantitative RT-PCR

Journal: bioRxiv

Article Title: Manganese mediates antiviral effects by driving an ATM-TBK1 phosphorylation signaling pathway

doi: 10.1101/2025.08.20.671272

Figure Lengend Snippet: ATM KO 293T cells were overexpressed by transfecting plasmids encoding wild type ATM (wt ATM), mutated ATM at kinase domain (ATM kd), mutated ATM at S1981A (ATM S1981A), respectively, and treated with Mn at varying concentrations. The total cell lysate was collected at 24 h after Mn treatment and subjected to western blot analysis using anti-ATM, p-TBK1, TBK1 antibodies, anti-β-actin was included as internal loading control. Untransfected 293T cells were also included in the experiment to serve as a positive control.

Article Snippet: The plasmids pcDNA3.1(+) Flag-His-ATM wild-type (wt), pcDNA3.1(+) Flag-His-ATM kinase-dead (kd), and hATM-S1981A (Addgene, Watertown, MA, USA) were used to overexpress either wild-type or mutant forms of ATM.

Techniques: Western Blot, Control, Positive Control