Journal: Cell reports

Article Title: Cardiolipin-mediated PPARγ S112 phosphorylation impairs IL-10 production and inflammation resolution during bacterial pneumonia

doi: 10.1016/j.celrep.2021.108736

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Chromatin immunoprecipitation experiments were performed using Chromaflash High Sensitivity ChIP kit (Cat # P-2027-48, Epigentek, USA) following the manufacturer’s instructions.

Techniques: Sequencing, Virus, Recombinant, In Vivo, Transfection, Concentration Assay, Protease Inhibitor, Lysis, Enzyme-linked Immunosorbent Assay, Immunoprecipitation, Isolation, Reverse Transcription, Mutagenesis, esiRNA, Control, Synthesized, Plasmid Preparation, Software

Journal: The Journal of Biological Chemistry

Article Title: An epigenetic regulatory loop controls pro-osteogenic activation by TGF-β1 or bone morphogenetic protein 2 in human aortic valve interstitial cells

doi: 10.1074/jbc.M117.783308

Figure Lengend Snippet: TGF-β1 and BMP-2 down-regulate miR-204 in AVICs via specific Smad pathways. A, human AVICs were treated with Smad1 siRNA, Smad3 siRNA, or scrambled siRNA (50 nm each) for 48 h before being exposed to TGF-β1 or BMP-2 for 24 h. Smad1 siRNA reduced Smad1 levels, but had no effect on Smad3 levels. Smad3 siRNA reduced Smad3 levels without an influence on Smad1 levels. Real-time quantitative RT-PCR analysis show that knockdown of Smad3 and Smad1 attenuates miR-204 down-regulation by TGF-β1 and BMP-2, respectively. n = 5 separate experiments using distinct cell isolates; *, p < 0.05 versus untreated control; #, p < 0.05 versus TGF-β1 alone or BMP-2 alone; ‡, p < 0.05 versus stimulant + scrambled siRNA. B, AVICs were stimulated with TGF-β1 or BMP-2 for 8 h and harvested for ChIP assay. ChIP DNA was amplified using specific primers for the miR-204 gene promoter after immunoprecipitation with antibodies against Smad1 (Ab-Smad1), Smad3 (Ab-Smad3), non-immune IgG (negative control), or RNA polymerase II (positive control). Input chromatin isolated before the immunoprecipitation was used to control for equal amounts of input DNA. Results of ChIP assay show that Smad1 and Smad3 can bind to the promoter region of miR-204 gene.

Article Snippet: Chromatin was prepared from human AVICs and ChIP was performed using ChromaFlash TM Chromatin Extraction Kit and ChIP Assay Kit according to the manufacturer's instruction (Epigentek Group Inc.).

Techniques: Quantitative RT-PCR, Knockdown, Control, Amplification, Immunoprecipitation, Negative Control, Positive Control, Isolation

Journal: Critical reviews in clinical laboratory sciences

Article Title: Epigenetic biomarkers: Current strategies and future challenges for their use in the clinical laboratory

doi: 10.1080/10408363.2017.1410520

Figure Lengend Snippet: Epigenetic biomarkers (cf(methylated)DNA, histones, and miRNAs) analyzed from multiple biospecimens (i.e. liquid biopsy, fresh tissue, and FFPE tissue) may allow simultaneous conduction of diagnosis and targeted therapy, therefore, contributing to theragnosis and precision medicine.

Article Snippet: The method is basically the same as those described by Shechter et al. [ 66 ], with the exception of the use of the hypotonic lysis buffer which is not required for serum samples. table ft1 table-wrap mode="anchored" t5 Table 3. caption a7 Kit name Manufacturer Biological source Downstream uses Chromatrap® FFPE ChIP Chromatrap FFPE tissue qPCR, sequencing ChIP-IT® FFPE Active Motif FFPE tissue qPCR, sequencing EPIXTRACT® kits Enzo Mammalian cells and tissues, plasma - serum, nuclear proteins Functional studies (WB, PTMs, enzymatic analysis) Histone extraction kit Abcam Mammalian cells and tissues Functional studies (WB, PTMs analysis) EpiQuik total histone extraction kit Epigentek Mammalian cells and tissues Functional studies (WB, PTMs analysis) ChromaFlash chromatin extraction kit Epigentek Cultured cells, fresh, and frozen tissue ChIP, in vitro protein-DNA binding assays and nuclear enzyme assays EZExtractTM core histone isolation kit BioVision Tissues and cultured cells Protein profiling, post-translational modification and epigenetic analyses Open in a separate window Chromatrap® (Porvair Sciences, Norfold, UK); ChIP-IT® (Active Motif.

Techniques: Methylation, Biomarker Discovery, Clinical Proteomics

Journal: Critical reviews in clinical laboratory sciences

Article Title: Epigenetic biomarkers: Current strategies and future challenges for their use in the clinical laboratory

doi: 10.1080/10408363.2017.1410520

Figure Lengend Snippet: Commercial kits and main characteristics of seven kits designed for whole chromatin or core histones isolation and purification from different biological sources.

Article Snippet: The method is basically the same as those described by Shechter et al. [ 66 ], with the exception of the use of the hypotonic lysis buffer which is not required for serum samples. table ft1 table-wrap mode="anchored" t5 Table 3. caption a7 Kit name Manufacturer Biological source Downstream uses Chromatrap® FFPE ChIP Chromatrap FFPE tissue qPCR, sequencing ChIP-IT® FFPE Active Motif FFPE tissue qPCR, sequencing EPIXTRACT® kits Enzo Mammalian cells and tissues, plasma - serum, nuclear proteins Functional studies (WB, PTMs, enzymatic analysis) Histone extraction kit Abcam Mammalian cells and tissues Functional studies (WB, PTMs analysis) EpiQuik total histone extraction kit Epigentek Mammalian cells and tissues Functional studies (WB, PTMs analysis) ChromaFlash chromatin extraction kit Epigentek Cultured cells, fresh, and frozen tissue ChIP, in vitro protein-DNA binding assays and nuclear enzyme assays EZExtractTM core histone isolation kit BioVision Tissues and cultured cells Protein profiling, post-translational modification and epigenetic analyses Open in a separate window Chromatrap® (Porvair Sciences, Norfold, UK); ChIP-IT® (Active Motif.

Techniques: Isolation, Purification, Sequencing, Clinical Proteomics, Functional Assay, Extraction, Cell Culture, In Vitro, Binding Assay, Modification

Journal: Critical reviews in clinical laboratory sciences

Article Title: Epigenetic biomarkers: Current strategies and future challenges for their use in the clinical laboratory

doi: 10.1080/10408363.2017.1410520

Figure Lengend Snippet: Proposed miRNAs used as endogenous control in RT-qPCR assays for detecting circulating miRNAs in liquid biopsy.

Article Snippet: The method is basically the same as those described by Shechter et al. [ 66 ], with the exception of the use of the hypotonic lysis buffer which is not required for serum samples. table ft1 table-wrap mode="anchored" t5 Table 3. caption a7 Kit name Manufacturer Biological source Downstream uses Chromatrap® FFPE ChIP Chromatrap FFPE tissue qPCR, sequencing ChIP-IT® FFPE Active Motif FFPE tissue qPCR, sequencing EPIXTRACT® kits Enzo Mammalian cells and tissues, plasma - serum, nuclear proteins Functional studies (WB, PTMs, enzymatic analysis) Histone extraction kit Abcam Mammalian cells and tissues Functional studies (WB, PTMs analysis) EpiQuik total histone extraction kit Epigentek Mammalian cells and tissues Functional studies (WB, PTMs analysis) ChromaFlash chromatin extraction kit Epigentek Cultured cells, fresh, and frozen tissue ChIP, in vitro protein-DNA binding assays and nuclear enzyme assays EZExtractTM core histone isolation kit BioVision Tissues and cultured cells Protein profiling, post-translational modification and epigenetic analyses Open in a separate window Chromatrap® (Porvair Sciences, Norfold, UK); ChIP-IT® (Active Motif.

Techniques: Control, Infection, Virus, Clinical Proteomics

Journal: Life

Article Title: Early-Life Stress Induced Epigenetic Changes of Corticotropin-Releasing Factor Gene in Anorexic Low Body Weight–Selected Chicks

doi: 10.3390/life10050051

Figure Lengend Snippet: Relative fold enrichment of DNA recovered from anti-MBD2 antibody-bound chromatin in the hypothalamus of non-stressed (NS) and stressed (S) LWS chicks on day 5 post-hatch. Data (n = 10 for NS and n = 12 for S) were analyzed by t -tests and are presented as means ± SEM. * p < 0.05.

Article Snippet: Then, 49 μL of sheared chromatin together with 1 μg of anti-methyl binding domain protein 2 (MBD2) antibody (Sigma) were used for each ChIP reaction using ChromaFlash One-Step ChIP kit (Epigentek) according to the manufacturer’s instructions.

Techniques: