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ETEC H10407 ChIP-Seq

ABSTRACT: ETEC H10407 ChIP-Seq

PROVIDER: PRJEB7505 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR654286.fastq.gz	Fastqsanger.gz
	ERR654287.fastq.gz	Fastqsanger.gz
	ERR654288.fastq.gz	Fastqsanger.gz
	ERR654289.fastq.gz	Fastqsanger.gz
	ERR654290.fastq.gz	Fastqsanger.gz

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Escherichia coli ETEC H10407

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Global transcriptome of CFA/I expressing ETEC H10407 under in vitro growth and water stress

Project description:Enterotoxigeneic Escherichia coli (ETEC) is a leading cause of diarrhoeal infections in young children living in endemic regions in low and middle-income countries and adults travelling to these destinations. CFA/I fimbriae have been identified as the predominant colonisation factor associated with human ETEC infections. Here we used used Transposon-directed insertion-site sequencing (TraDIS) and transcriptomic analysis to identify the essential genome of the prototypical CFA/I expressing ETEC strain H10407 and uncover the survival mechanisms that enhance persistence of ETEC isolates in water and within mammalian hosts. RNA transcription profiles of H10407 were identified under different in vitro growth conditions including aerobic growth in neutral LB media (pH7); aerobic growth in acidic media (pH5); aerobic growth in alkaline media (pH9); anaerobic growth in neutral LB media (pH7); and survival in fresh water. Research work including RNA preparation and bioinformatics and statistical analyses were conducted at the Wellcome Trust Sanger Institute (WTSI) and the Westmead Institute for Medical Research (WIMR), the University of Sydney. The sequencing data was generated in the Bioscience Core Laboratory at King Abdullah University of Science and Technology (KAUST).

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ETEC H10407 ChIP-Seq

Project description:To generate and compile data from ChIP-Seq libraries. Looking at CRP, H-NS, and sigma70 binding genome wide under M9 minimal growth conditions in duplicate.

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Project description:The experiment contains ChIP-seq data for Enterotoxigenic Escherichia coli strain H10407 transformed with plasmids pAMNF (encoding an N-terminal MarR-3xFLAG fusion) or pAMNM (encoding an N-terminal MarR-8xmyc fusion). The cells was cultured at 37 degrees in LB medium and crosslinked with 1 % (v/v) formaldehyde. After sonication, to break open cells and fragment DNA, immunoprecipitations were done using an anti-FLAG antibody (i.e. the strain encoding the MarR-8xmyc fusion was used as a control). Libraries were prepared using DNA remaining after immunoprecipitation.

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ChIP-seq of the multiple antibiotic resistance activator (MarA) protein and RNA polymerase sigma70 subunit of Enterotoxigenic Escherichia coli strain H10407

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