ChIP-seq of budding yeast cells for the genomic maps of Mediator, Rad2, Rad3, RNA Pol II, TBP and TFIIH to study the functional link between Rad2 and Mediator
ABSTRACT: In this study, we generate genomic maps of Mediator, Rad2, Pol II, TBP and TFIIH, by ChIP coupled to next generation sequencing technology (ChIP-seq), in wild type strains from Saccharomyces cerevisiae. A related study involving ChIP-chip analysis of Rad2 occupany is also deposited at ArrayExpress under accession number E-MEXP-3875 ( http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3875 ).
INSTRUMENT(S): Illumina Genome Analyzer II, Illumina HiSeq 2000
Project description:In this study, we generate genomic maps of Mediator, Pol II, TBP and TFIIH, by ChIP coupled to next generation sequencing technology (ChIP-seq), in wild type (WT) strains and med17-ts mutants from Saccharomyces cerevisiae. Some of the data, concerning WT strains are also deposited at ArrayExpress under accession number E-MTAB-1595 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1595). There are 2 series of experiment: 1- WT (see E-MTAB-1595) and mutants med17-98, med17-444, and med17-670 (this submission) 2- WT and mutant med17-444 (this submission).
Project description:In this study, we generate genomic maps of Mediator, Pol II, TBP, TFIIH, TFIIA, TFIIB, TFIIE, TFIIF, by ChIP coupled to next generation sequencing technology (ChIP-seq), in wild type strains from Saccharomyces cerevisiae and in a mutant for the Mediator essential subunit Med10
Project description:This aim of this experiment is to assess the genome-wide Rad2 occupancy in yeast Saccharomyces cerevisiae by ChIP-chip, in the absence of exogenous genotoxic stress. A related study involving ChIP-seq analysis of Rad2 occupany is also deposited at ArrayExpress under accession number E-MTAB-1595 ( www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1595 ).
Project description:HilD is a regulator of Salmonella pathogenicity island 1 (SPI-1) virulence genes in Salmonella enterica serovar Typhimurium. To identify novel HilD-regulated genes, we mapped the genome-wide association of HilD in S. Typhimurium under SPI-1-inducing conditions (high salt, low aeration) using ChIP-seq. HilD was C-terminally tagged with 3 FLAG tags in strain 14028s.
Project description:We mapped the genome-wide binding of the flagellar regulators FlhD, FlhC, and FliA in FLAG-tagged derivatives of E. coli K-12 MG1655 using ChIP coupled with deep sequencing (ChIP-seq). We identify new binding sites for each factor.
Project description:A defining characteristic of quiescent cells is their low level of gene activity compared to growing cells. Using a yeast model for cellular quiescence, we compared the genome-wide profiles of multiple histone modifications between growing and quiescent cells, and correlated these profiles with the presence of RNA polymerase II and its transcripts. Quiescent cells retained several forms of histone methylation normally associated with transcriptionally active chromatin and had many transcripts in common with growing cells. Quiescent cells also contained high levels of RNA polymerase II, but only low levels of the canonical initiating and elongating forms of the polymerase. The data suggest that the transcript and histone methylation marks in quiescent cells were either inherited from growing cells or established early during the development of quiescence and then retained in this non-growing cell population. This might ensure that quiescent cells can rapidly adapt to a changing environment to resume growth. Immunoprecipitation experiments were carried out for Pol II, H3K36me3, H3K4me3, H3K79me3 and H3 separately using both Log-phase and Quiescent cells. Each ChIP-chip assay was conducted using a control (IN) and in all instances, at least one replicate experiment was performed.