Project description:Quantitation the lysine 2-hydroxyisobutyrylation of H-NS in TmcA KO and YiaC KO E. coli strains using PRM. PRM was performed on an Orbitrap Q Exactive Plus mass spectrometer with an EASY-Spray source coupled to a Nano-LC system (EASY-nLC 1000, Thermo Fisher Scientific, Waltham, MA).
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived heart transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: myocardium mRNA profiles of 6-week-old wild-type (WT) and whole-body knock-in mutations in DADs of both NCOR and SMRT (NS-DADm) mice were generated by Agilent 2100 Bio analyzer. we filter the low quality reads (More than 20% of the bases qualities are lower than 10),reads with adaptors and reads with unknown bases (N bases more than 5%)to get the clean reads. Then we map those clean reads onto reference genome, followed with novel gene prediction, SNP &INDEL calling and gene splicing detection. Finally, we identify DEGs (differentially expressed genes) between samples and do clustering analysis andfunctional annotations Results: Using an optimized data analysis workflow, we find genes upregulated and enriched in NS-DADm myocardium that were consistent with HDAC3 inhibitor treated heart compared with WT Conclusions: Our study represents the first detailed analysis of genes expression in myocardium of HDAC3 enzymatic activity-dead NS-DADm mice
Project description:Transcriptional profiling of squamous cell carcinoma of oral tongue, comparing p53 NS+ and p53 NS- tumors. Goal was to determine differentially expressed genes between them based on global gene expression.
Project description:To study the effect of the ACVR1 G328V mutation in tumor neurospheres with a background of NRASV12 overexpression and p53 knockdown. The goal of this study was to identify differentially expressed genes between mACVR1 NS v wt-ACVR1 NS.
Project description:Transcriptional profiling of Esophageal Squamous Cell Carcinoma (ESCC) tumors comparing samples harbouring nuclear-stabilized p53 (NS+) versus unstable p53 (NS-) protein, determined through immunohistochemistry (IHC) staining of the tumor sections. The goal was to identify the genes that were differentially regulated between NS+ and NS- ESCC samples.
Project description:To reveal the functional consequences of H-NS modifications, we performed proteome and secretome of Salmonella wild-type and H-NS mutant strains to analyze how phosphorylation impacts the landscape of H-NS-regulated bacterial proteins.
Project description:This study aims to investigate lysine acetylation sites on the H-NS protein in Edwardsiella piscicida. The H-NS protein was first purified, then subjected to SDS-PAGE, followed by gel band excision and LC-MS/MS identification.
Project description:We performed single cell RNA sequencing to analyze the transcriptional profile of gliogenic NS/PCs and neurogenic NS/PCs derived from the same parental feeder-free iPSCs.