E-ERAD-177 - Methylation profiling of Escherichia coli to investiagte variation of DNA damage and repair along a bacterial genome

Status
Released on 2 December 2013, last updated on 10 December 2013
Organism
Escherichia coli str. K-12 substr. MG1655
Samples (9)
Protocols (2)
Description
Recent evidence from cancer and bacterial genome sequencing studies evidences that the mutation rate varies largely along a genome, suggesting that the activity of DNA mutagenesis and repair is different in different regions of a genome. Unfortunately, while decades of research on the field of DNA mutagenesis and repair have yielded a detailed molecular understanding of these processes, we know virtually nothing about their variable activity along a genome. A major reason for this is the lack of functional genomic techniques to study DNA mutagenesis and DNA repair along the genome, which contrasts with the impact of genomics in other fields such as transcriptional regulation and epigenetics. We have now successfully used DNA immunoprecipitation to isolate DNA fragments carrying 8-oxoguanine sites (one of the major oxidative lesions) using a protocol similar to certain MEDIP-seq protocols used to identify methylated DNA. These DNA fragments will then be sequenced and mapped to the reference genome, obtaining a map of the relative rate of DNA oxidative damage along the E.coli genome. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Experiment type
methylation profiling by high throughput sequencing 
Contact
MINSEQE
Exp. designProtocolsFactorsProcessedSeq. reads
Files
Investigation descriptionE-ERAD-177.idf.txt
Sample and data relationshipE-ERAD-177.sdrf.txt
Links