Project description:This dataset contains ChIP-seq data of H3K4me3 and Pol III in single cell-derived control and CRISPR/Cas9 induced tRNA gene deletion clones in human cancer cell lines HAP1 and HepG2. In this study, we looked into functional Cas9-induced on-target genomic alteration in our tRNA gene deletion clones, HAP1 t72 and HepG2 t15.
Project description:The genomic loci occupied by RNA polymerase (pol) III have been characterized in human culture cells by genome-wide chromatin immunoprecipitation experiments followed by deep sequencing (ChIP-Seq). These studies have in particular shown that only about 40 % of the annotated 622 human tRNA genes and pseudogenes are occupied by pol III, and that these genes are often in regions of open chromatin rich in active pol II transcription units. Here we have used ChIP-Seq to characterize pol III-occupied loci in a differentiated tissue, the mouse liver. Our studies define the mouse liver pol III-occupied loci and point to a conserved pol III-occupied mammalian interspersed repeat (MIR) as a potential regulator of a pol III subunit-encoding gene. They reveal that synteny relationships can be established between a number of human and mouse pol III genes, and that the expression levels of these genes are significantly linked. They establish that variations within the A and B promoter boxes, as well as the strength of the terminator sequence can strongly affect pol III occupancy of tRNA genes. They reveal correlations with various genomic features that together describe the pol III occupancy scores over some 50% of tRNA genes. In mouse liver, pol III-occupied loci represented in the NCBI37/mm9 genome assembly comprise fifty 5S genes, fourteen known non-tRNA genes, nine 4.5S genes, and some twenty nine SINEs. In addition, out of the 433 annotated tRNA genes, half are occupied by pol III. Transfer RNA gene expression levels reflect both an underlying genomic organization that is conserved in dividing human culture cells and resting mouse liver cells, and the particular promoter and terminator strengths of individual genes. 12 samples examinded, 4 on pol III, 2 on pol II, 2 on H3K4me3, 2 on H3k36me3, 2 input samples.
Project description:The tRNA gene expression change was evaluated by whole genomic microarray chip in Streptococcus oligofermentans challenged by H2O2.
Project description:This dataset contains ChIP-seq data profiling genomic binding of H3K27ac and H3K4me3 in single cell-derived control, as well as CRISPR/Cas9 induced tRNA gene deletion clones and intergenic region deletion clones in human cancer cell lines HAP1. In this study, we found a large genomic deletion of 10q23 in Cas9 modified clones and further investigate the effect of H3K27ac binding.
Project description:This dataset contains Xdrop followed by oxford nanopore long read sequencing performed in target tRNA gene deletion clones in HAP1 (t72) and HepG2 (t15). By applying de novo assembly based approach to Xdrop-LRS data, we identified Cas9-induced on-target genomic alteration.
Project description:This dataset contains Xdrop followed by oxford nanopore long read sequencing performed in target tRNA gene deletion (t8) and intergenic region deletion (i50) clones in HepG2 . By applying de novo assembly based approach to Xdrop-LRS data, we identified Cas9-induced on-target genomic alteration.
Project description:Interventions: Genomic test CANCERPLEX-JP OncoGuide NCC oncopanel system FndationONe CDx genome profile GUARDANT360 MSI Analysis System BRACAnalysis
Primary outcome(s): Development of genome database
Study Design: Single arm Non-randomized
