Project description:RNAseq replicate in Proliferating and Senescent IMR90s We used RNAseq to examine RNA levels in human IMR90 replicative senescence (RS)
Project description:H3K9me3 ChIPseq in Proliferating and Senescent IMR90s We used ChIP-seq to examine the global binding of H3K9me3 in human IMR90 replicative senescence (RS) and oncogene-induced (OIS)
Project description:To investigate the molecular basis of senescence-induced dedifferentiation, we performed RNAseq on control proliferating cells (DMSO only) and etoposide-induced senescent cells to profile senescence induction. Additionally, we performed RNAseq on purified populations of differentiated myotubes derived from untreated A1 cells to investigate differentiation, as well as myotubes subsequently induced to dedifferentiate, either by serum exposure (10% FCS) or by exposure to 48 hour conditioned media from senescent cells (including proliferating cell conditioned media controls). We then performed gene expression profiling analysis using data obtained from RNA-seq of all 6 populations in triplicate.
Project description:In this study, we examined the reproducibility of nucleotide variant calls in replicate sequencing experiments of the same genomic DNA. We performed targeted sequencing of all known human protein kinase genes (kinome) (~3.3 Mb) using the SOLiD v4 platform. Seventeen breast cancer samples were sequenced in duplicate (n=14) or triplicate (n=3) to assess concordance of all calls and single nucleotide variant (SNV) calls.
Project description:MotivationWhile classical approaches for controlling the false discovery rate (FDR) of RNA sequencing (RNAseq) experiments have been well described, modern research workflows and growing databases enable a new paradigm of controlling the FDR globally across RNAseq experiments in the past, present and future. The simplest analysis strategy that analyses each RNAseq experiment separately and applies an FDR correction method can lead to inflation of the overall FDR. We propose applying recently developed methodology for online multiple hypothesis testing to control the global FDR in a principled way across multiple RNAseq experiments.ResultsWe show that repeated application of classical repeated offline approaches has variable control of global FDR of RNAseq experiments over time. We demonstrate that the online FDR algorithms are a principled way to control FDR. Furthermore, in certain simulation scenarios, we observe empirically that online approaches have comparable power to repeated offline approaches.Availability and implementationThe onlineFDR package is freely available at http://www.bioconductor.org/packages/onlineFDR. Additional code used for the simulation studies can be found at https://github.com/latlio/onlinefdr_rnaseq_simulation.Supplementary informationSupplementary data are available at Bioinformatics online.