p53 transcriptional programs in B cells upon exposure to genotoxic stress in vivo: Computational analysis of next-generation sequencing data

Claudia Tonelli; Bruno Amati; Marco J Morelli

doi:10.1016/j.gdata.2015.11.006

p53 transcriptional programs in B cells upon exposure to genotoxic stress in vivo: Computational analysis of next-generation sequencing data

Genom Data. 2015 Nov 7:7:29-31. doi: 10.1016/j.gdata.2015.11.006. eCollection 2016 Mar.

Authors

Claudia Tonelli¹, Bruno Amati², Marco J Morelli³

Affiliations

¹ Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, 20139 Milan, Italy.
² Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, 20139 Milan, Italy; Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy.
³ Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy.

Abstract

The transcriptional programs activated by p53 in B cells in vivo following exposure to ionizing radiation were studied through the integrated analysis of various types of next-generation sequencing data: genome-wide profiling of p53 binding sites, mapping of histone marks and open chromatin regions and quantification of gene expression. Moreover, the binding of p53 was associated to a series of specific motifs on the DNA, which were directly inferred from the data. Here, we describe in detail the computational analysis of the datasets associated with our study (Tonelli et al., Oncotarget 6 (2015), 24611-26), deposited in the GEO archive (accession code GSE71180), and we provide the R scripts needed to generated the figures of the paper.

Keywords: ChIP-Seq; Genotoxic stress; Motif analysis; RNA-Seq; p53.