Project description:Control and RBM6-KO MCF10A-Hras cells were subjected to RNA-sequencing before and after 12hrs exposure to 5Gy ionizing radiation (IR). Transcriptome analysis revealed a subset of genes that are differentially regulated in RBM6-KO cells compared to control cells. In addition, transcriptome of RBM6-KO cells after IR showed upregulation of DNA damage genes, suggesting impaired DNA repair compared to control cells.
Project description:Gene expression analysis of BJhTERT RhoA-KO and PC3 mRFP was performed before and after six days confrontation in co-cultivation. Analyses of original and control fibroblasts was also performed. To identify molecules that may mediate the tumor promoting effect of RhoA knock out fibroblasts, we performed gene expression analysis of BJhTERT RhoA-KO and PC3 mRFP cells before the confrontation and then after six days after it, using Affymetrix Whole Transcript Assay platform.
Project description:Gene expression profiling of ISWI chromatin remodeler mutants before and after DNA damage BAZ1A is a regulatory subunit within the ISWI family of chromatin remodelers in humans. We and others have shown that BAZ1A is required for efficient recovery from DNA damage. The DNA damage hypersensitivity caused by BAZ1A* is as severe as the deletion of the entire gene. This is striking given that BAZ1A* contains only two substitutions (K1181A and K1183Y) within a poorly characterized domain of BAZ1A. We find that this domain can interact with DNA, and that the mutations present in BAZ1A* hinder DNA binding. We used transcriptional profiling to identify molecular events leading to the DNA damage hypersensitivity of BAZ1A* cells.
Project description:Transcriptional profiling of human fibroblast cells after DNA damage with Camptothecin or Etoposide or Neocarzinostatin Upon DNA damage, the DNA damage response (DDR) elicits a complex signaling cascade, which includes the induction of multiple non-coding RNA species. Recently long non-coding RNAs (lncRNAs) have been shown to contribute to DDR by regulating gene expression. However, very little is known about the role that lncRNAs play in regulating DNA Repair. Using a genome-wide microarray screen we identified a novel ubiquitously expressed lncRNA, DDSR1 (DNA damage-sensitive RNA 1), which is induced upon DNA damage by several DNA double-strand break (DSB) agents. Two-condition experiment, Control vs. DNA damage human fibroblast cells. No Replicates, DNA damage was induced with either Camptothecin or Etoposide or Neocarzinostatin, Total RNA or Nuclear RNA was profiled.
Project description:To model and characterize the chromatin regulatory landscape in Neural stem cell before and after Phf2 knockout, we performed HiC to map large-scale 3D architectural rewiring in WT and Phf2-KO NSC.
Project description:This first-in-human (FIH) dose-escalation and dose-validation/expansion study will assess KO-2806, a farnesyl transferase inhibitor (FTI), as a monotherapy and in combination, in adult patients with advanced solid tumors.
Project description:Gene expression analysis of BJhTERT RhoA-KO and PC3 mRFP was performed before and after six days confrontation in co-cultivation. Analyses of original and control fibroblasts was also performed. To identify molecules that may mediate the tumor promoting effect of RhoA knock out fibroblasts, we performed gene expression analysis of BJhTERT RhoA-KO and PC3 mRFP cells before the confrontation and then after six days after it, using Affymetrix Whole Transcript Assay platform. Four days old fibroblast monolayer was confronted with PC3 mRFP tumor cells, plated in ratio 1:30 to number of plated fibroblasts. After six days of confrontation cells were sorted by FACS (Fluorescence-activated cell sorting). Total RNA was isolated from each confronted and non-confronted cells with kit. Then 150 ng of total RNA were used for transcriptomic analysis.for RNA extraction and hybridization on Affymetrix microarrays