Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ChIP-chip by array of yeast strains BY and RM after TSA treatment and recovery using anti-H3K14ac polyclonal antibody to investigate the stability of chromatin acetylation epi-polymorphisms

ABSTRACT: Strains BY and RM were cultivated with high concentrations of Trichostatin-A (TSA) and then let recover for >20 generations before re-profiling H3K14ac by ChIP as in Nagarajan et al. 2010 PLoS Genetics

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Gael Yvert

PROVIDER: E-MTAB-1025 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Genetic modifiers of chromatin acetylation antagonize the reprogramming of epi-polymorphisms.

Abraham Anne-Laure AL Nagarajan Muniyandi M Veyrieras Jean-Baptiste JB Bottin Hélène H Steinmetz Lars M LM Yvert Gaël G

PLoS genetics 20120920 9

Natural populations are known to differ not only in DNA but also in their chromatin-associated epigenetic marks. When such inter-individual epigenomic differences (or "epi-polymorphisms") are observed, their stability is usually not known: they may or may not be reprogrammed over time or upon environmental changes. In addition, their origin may be purely epigenetic, or they may result from regulatory variation encoded in the DNA. Studying epi-polymorphisms requires, therefore, an assessment of t ...[more]

PMID: 23028365

Similar Datasets

Temporal Expression Profiling Identifies Pathways Mediating Effect of Causal Variant on Phenotype

Project description:Temporal expression profiling during sporulation for MKT1 allele replacement strains in S288c

2015-04-18 | E-MTAB-3454 | biostudies-arrayexpress

Investigating the role of a coding polymorphism in TAO3 in sporulation efficiency variation in yeast

Project description:Temporal expression profiling during sporulation for TAO3(4477C) allele replacement strains in S288c. Raw gene expression data CEL files for control TAO3(4477G) allele strain are given in E-MTAB-3454 (see 9 array files from \S_Spo0h0m_Scerevisiae_tlg.CEL\ to \S_Spo8h30m_Scerevisiae_tlg.CEL\).

2015-12-31 | E-MTAB-3889 | biostudies-arrayexpress

Effect of stress on the binding affinity of yeast eIF4F components to their target RNAs

Project description:Translation factors eIF4E and eIF4G form eIF4F, which binds to mRNAs to promote ribosome recruitment and translation initiation. We were interested in analysing the effects of stresses on eIF4F interactions with individual mRNAs. We used a RIP-seq approach to assess how mRNA associations with eIF4E, eIF4G1 and eIF4G2 change in response to three stresses: 1) addition of hydrogen peroxide; 2) amino acids withdrawal; and, 3) glucose withdrawal. We find that acute stress leads to changes in eIF4FmRNA interactions that are shared among each factor and across the stresses imposed.

2017-10-11 | E-MTAB-5836 | biostudies-arrayexpress

Control of Virulence Gene Expression in Citrobacter rodentium by Trascription Factor RegA

Project description:Identification of the targets of RegA with and without bicarbonate stimulation by comparing RegA knockout to multicopy RegA transgenics. RegA is an AraC like transcription factor identified in a mutational screen for virulence genes in Citrobacter rodentium, an attaching and effacing pathogen that causes transmissible colonic hyperplasia in mice. This experiment compares the RegA null strain with a multicopy plasmid rescue of this null strain in the presence and absence of bicarbonate with the aim of identifying pathogenesis related genes related to the early and late stages of attachment and effacement. Keywords: genetic modification, transcription factor, induction A strain of Citrobacter rodentium with a knockout of RegA was compared to the same strain rescued with a multicopy plasmid containing the wildtype RegA gene. These strains were analyzed with and without bicarbonate in an unconnected two factor design with dye balanced biological replicates.

2010-05-19 | E-GEOD-12876 | biostudies-arrayexpress

RNA sequencing of pheromone stimulated and unstimulated MATa and MATM-NM-1 Saccharomyces cerevisiae

Project description:Haploid budding yeast has two mating types, defined by the alleles of the MAT locus, MATa and MATM-NM-1. Mating occurs when two haploid cells of opposite mating types signal to each other using reciprocal pheromones and receptors, polarize and grow towards each other, and eventually fuse to form a single diploid cell. The pheromones and receptors are necessary and sufficient to define a mating type, but other mating type-specific proteins make mating more efficient. We examined the role of these proteins by genetically engineering M-bM-^@M-^\transvestiteM-bM-^@M-^] cells that swap the pheromone, pheromone receptor, and pheromone processing factors of one mating type for another. These cells can mate with each other, but their mating is inefficient. By characterizing their mating defects and examining their transcriptomes, we found Afb1 (a-factor barrier), a novel MATM-NM-1-specific protein that interferes with a-factor, the pheromone secreted by MATa cells. We show that strong pheromone secretion is essential for efficient mating and that the weak mating of transvestites can be improved by boosting their pheromone production. Using synthetic biology, it is possible to characterize the factors that control efficiency in biological processes. In the case of budding yeast mating, selection for increased mating efficiency is likely to have continually boosted pheromone levels and the ability to discriminate between partners who make more (potentially fitter) and less (potentially less fit) pheromones. This sensitivity to which partner makes more pheromone comes at a cost: it means mating is not robust in situations where all potential partners make less pheromone. 4 conditions were analysed, each with 3 biological replicates. The conditions were unstimulated MATa cells in YPD. Stimulated MATa cells in YPD+10nM M-NM-1-factor. Unstimulated MATM-NM-1 cells in YPD. Stimulated MATM-NM-1 cells in YPD+10nM M-NM-1-factor.

2014-01-07 | E-GEOD-49372 | biostudies-arrayexpress

Context Dependent Effects of Ascorbic Acid Treatment in TET2 Mutant Myeloid Neoplasia

Project description:Loss-of-function TET2 mutations (TET2MT) are common in myeloid neoplasia. TET2, a DNA dioxygenase, requires 2-oxoglutarate and Fe(II) to oxidize 5-methylcytosine. TET2MT thus result in hypermethylation and transcriptional repression. Ascorbic acid (AA) increases dioxygenase activity by facilitating Fe(III)/Fe(II) redox reaction and may alleviate some biological consequences of TET2MT by restoring dioxygenase activity. Here, we report the utility of AA in the prevention of TET2MT MN, clarify the mechanistic underpinning of the TET2-AA interactions, and demonstrate that the ability of AA to restore TET2 activity in cells depends on N- and C-terminal lysine acetylation and nature of TET2MT. Consequently, pharmacologic modulation of acetyltransferases and histone deacetylases may regulate TET dioxygenase-dependent AA effects. Thus, our study highlights the contribution of factors that may enhance or attenuate AA effects on TET2 and provides a rationale for novel therapeutic approaches including combinations of AA with class I/II HDAC inhibitor or sirtuin activators in TET2MT leukemia.

2020-09-09 | PXD020550 | Pride

Environmentally persistent genetic associations with gene expression reveal pathways mediating genetic signals to phenotype

Project description:Unraveling the causal chain of biochemical events that link genotype to phenotype is critical for understanding the molecular basis of genetic diseases and for designing personalized drug therapies. To this end, using yeast as a model system, we carried out joint profiling of fitness and gene expression. Transcription profile includes 4 media (YPD (YPE, YPMalt, YPE and YPD_BPS) of ~35 segregants spores each media were obtained from a cross of the yeast strains S96 and YJM789. These spores are a subset of those published by Mancera et al, Nature, 2008. Sufficient cells were grown at 30 °C in media of interest to the mid log phase. After harvest, gene expression profiling were performed using tiling array as previous described (Xu et al, Nature, 2009). The expression level of each transcript was used as molecular trait for further investigation in the study. 1 CEL data files was mislabelled: 110427_09C_BPS_(Scerevisiae_tlg).CEL.gz, actually spores 09D. The correct spore IDs are in the sample annotation (under StrainOrLine or sample name).

2013-08-12 | E-MTAB-1398 | biostudies-arrayexpress

Expression-profiling of the Mediator transcription complex

Project description:Proteins from within the Saccharomyces cerevisiae Mediator transcription complex were knocked out and compared against wild type yeast using two-color oligo arrays.

2005-08-15 | E-UMCU-20 | biostudies-arrayexpress

Analysis of the evolutionary adaptation of an AraC-like global regulatory protein in the murine enteric pathogen Citrobacter rodentium

Project description:An experiment to test the equivalence of the Citrobacter rodentium RegA and E.Coli SMS 3-5 homologue 8 Conditions (4 Genotypes by 2 treatments) in duplicate. Reference design without dye swaps.

2015-02-19 | E-GEOD-57689 | biostudies-arrayexpress

The RegR virulence regulon of rabbit specific enteropathogenic Escherichia coli strain E22

Project description:To investigate the regulatory targets of the RegR virulence regulon of rabbit specific enteropathogenic Escherichia coli strain E22 Single factor (genotype) with dye swaps.

2012-12-25 | E-GEOD-41093 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data