Project description:In vitro pull down assay was performed using recombinant GST and GST fusion SOX2 protein to precipitate total RNA from urothelial carcinoma cell line BFTC905 Unbound RNA from both reactions and matrix-associated RNA from SOX2 pull down reaction was extracted using TRIZOL reagent
Project description:GST pull-down assay using crude extracts from HCT116 cells to analyze the selectivity of the UFD1-NBM peptide in a cellular context.
Project description:In vitro pull down assay was performed using recombinant GST and GST fusion SOX2 protein to precipitate total RNA from urothelial carcinoma cell line BFTC905 Unbound RNA from both reactions and matrix-associated RNA from SOX2 pull down reaction was extracted using TRIZOL reagent This experiment is to identify mRNA bound by SOX2 under in vitro experimental condition
Project description:The TET3 CXXC domain has unique DNA binding properties. It binds to DNA in a cytosine-dependent manner that prefers binding to CpG dinucleotides but is not restricted by the CpG-content, distinct from other well-characterized CXXC domains. To map the TET3 CXXC domain binding sites across the human genome, we purified the GST-tagged TET3 CXXC domain protein and performed the GST pull-down assay using the genomic DNA purified from HEK293T cells. The enriched DNA fragments were then sequenced and aligned to human genome(hg19). We used the GST pull-down assay followed by DNA deep sequencing to map the DNA bound by the TET3 CXXC domain in vitro.
Project description:Bee venom has been traditionally used in the treatment of inflammatory disorders and is known to contain diverse bioactive peptide components. In this study, we systematically characterized the Apis mellifera venom peptidome and investigated peptides enriched under TRPV1 pull-down conditions with potential inflammatory modulatory activity. Crude venom was fractionated by AKTA chromatography, and individual fractions were evaluated by SDS–PAGE. Protein bands were subjected to in-gel digestion followed by LC–MS/MS protein identification. Fraction F4, which displayed a prominent A280 absorbance peak during AKTA chromatography, was further analyzed by LC–MS/MS–based peptidomics. De novo sequencing results from fraction F4 were used to construct an in-house custom peptide database. Two independent GST pull-down workflows (exploratory and in-house) were performed using GST-TRPV1 and GST controls. Candidate peptides enriched in the GST-TRPV1 pull-down relative to GST controls were identified following background subtraction and peak-area filtering criteria. Selected synthetic peptide candidates were subsequently evaluated using macrophage-based proteomics experiments to assess their potential inflammatory modulatory effects. The deposited dataset includes raw LC–MS/MS files and processed outputs for gel-based protein identification, venom peptidomics, pull-down–associated peptide identification, macrophage proteomics (MaxQuant analysis), and the custom venom peptide FASTA library used for database searches.
Project description:Genome-wide identification of R-loops almost uniquely relies on antibody based pull-down, a method that shows sequence and structural biases. Here we describe a novel approach – DREAM-seq – centered around the use of endonuclease digestions. Unstimulated and stimulated B cells showed that R-loops are more widespread than anticipated, mostly covering all actively transcribed genes.
Project description:A pull-down assay by incubating the His-tagged PPARalpha-LBD with various brain tissue (cortex, cerebellum, and hippocampus) extracts.