Project description:We performed ChIP-Sequencing for GR in GR wild-type, GR Zn mutant and GR Knock-Out Mouse Embryonic Fibroblasts (MEFs). We show that GR Zn mutant chromatin binding is mostly lost except for some tethered binding sites. Together with the corresponding RNA-Seq data, our results illustrate how GR requires direct DNA binding for activation and repression of target genes.
Project description:We investigated the genomewide binding pattern of prevalent p53 gain-of-function (GOF) mutants by ChIP-seq, in a panel of breast cancer cell lines. We assessed the genomewide changes of H3K4me3 upon GOF p53 knockdown in MDA-MB-468 breast cancer cells bearing the p53 R273H mutation. This study uses ChIP-seq of H3K4me3 and histone H3 in wild-type or p53 R172H knock-in MEFs. Additionally, this study examines the transcriptome of wild-type or p53 R172H knock-in MEFs using polyA+ RNA-seq.
Project description:Gene expression analysis of wild type, STING knock-out and STAT1 knock-out Mouse Embryonic Fibroblasts (MEFs) stimulated with 90-mer dsDNA or 90-mer ssDNA. Genes whose expression that are affected by cytosolic DNA in a STING dependent manner will be identified and signaling pathways regulated by STING will be elucidated.
Project description:We utilized precicion run-on sequencing (PRO-seq) to analyze the roles of HSF1 and HSF2 in the reprogramming of transcription under oxidative stress and heat shock. PRO-seq was performed in wild-type (WT), HSF1 knock-out (HSF1 KO) and HSF2 knock-out (HSF2 KO) mouse embryonic fibroblasts (MEFs) that were treated with heat shock (HS) or oxidative stress induced by menadione (MD).
Project description:<p>Gene expression is a biological process regulated at different molecular levels, including chromatin accessibility, transcription, and RNA maturation and transport. In addition, these regulatory mechanisms have strong links with cellular metabolism. Here we present a multi-omics dataset that captures different aspects of this multi-layered process in yeast. We obtained RNA-seq, metabolomics, and H4K12Ac ChIP-seq data for wild-type and mip6delta strains during a heat-shock time course. Mip6 is an RNA-binding protein that contributes to RNA export during environmental stress and is informative of the contribution of post-transcriptional regulation to control cellular adaptations to environmental changes. The experiment was performed in quadruplicate, and the different omics measurements were obtained from the same biological samples, which facilitates the integration and analysis of data using covariance-based methods. We validate our dataset by showing that ChIP-seq, RNA-seq and metabolomics signals recapitulate existing knowledge about the response of ribosomal genes and the contribution of trehalose metabolism to heat stress.</p>
Project description:Mta1 gene expression reveals new targets and functions. Mta1 functions in p53 dependent and independent manner. Genes regulated by Mta1 in the presence and absence of p53 were indetified This expression data contains 5 different samples (MEFs) 1.wild type 2. Mta1 knockout 3. Mta1 re-expression in the knock out MEFs 4. P53 knockout and 5. Mta1 over expression in P53 knock out MEFs. Various sample comparisons were done and genes with p-value< 0.05 and fold change ≥ 2.0 were considered statistically significant
Project description:Gene expression analysis of wild type and STING knock-out Mouse Embryonic Fibroblasts (MEFs) infected with γ34.5 deleted HSV1. Genes whose expression that are affected by HSV1 in a STING dependent manner will be identified and signaling pathways regulated by STING will be elucidated.
Project description:We performed a global mRNA expression profiling via RNA-seq. Genes differentially expressed in Mitf knock-in MEFs compared to vehicle-treated knock-in MEFs were clustered and compared to expression in untreated wild-type MEFs and primary mouse melanocytes. This clustering demonstrates a gradual transition in the expression profile of Dox-treated Mitf knock-in MEFs toward the melanocyte expression profile
