Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic analyses of three wine yeast strains duting their response to nitrogen availability

ABSTRACT: A time-course transcriptomic experiment was performed in three geographically different wine yeast strains in order to test differences in gene expression as response to different nitrogen availability mRNA amounts for different wine yeast strains at different nitrogen availability was determined along the fermentation of a syntethic must. mRNA determinations were made at different fermentation stages (12, 24, 36 and 96 h after innoculation) Please note that there are two replicates per each stage (i.e. two raw data files per each sample; R1.txt and R2.txt) and the data were combined to generate the normalized data for each stage (i.e. sample).

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Jose Perez-Ortin

PROVIDER: E-GEOD-63187 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Genomic Run On (GRO): determination of the nascent transcriptional rates in a spt16 mutant

Project description:We analyzed the effect of SPT16 on the transcription rates, mRNA stabilities and mRNA levels by doing GRO experiments in a thermosensitive spt16 point mutant (G132D) mutant at 35 ÂºC comparing with permisive temperature (30 ÂºC) and a wt treated in the same way. Cells (wt or spt16 mutant) were grown in SC-ura at 30 ÂºC to 0.25 OD600. At that time Î± factor was added and let to stand for 160 min in the same conditions. Then each sample (wt or mutant) was separated in two aliquots. One of them remain at 30ÂºC and the other was incubated at 35ÂºC. Both aliquots in the presence of Î± factor for 1h more. Finally, samples were processed for GRO experiment as described in Garcia-Marinez et al (2004). Three replicates of the whole experiment were done.

2016-01-05 | E-GEOD-64006 | biostudies-arrayexpress

Transcriptomic study in RNA pol II foot mutants

Project description:The goal of the project was to study the effects on transctiptome of some Rpb1 foot mutations that block Rpb4/7 assembly Cells were grown in YPD at 30ÂºC to 0.5 OD600. At that cells were spun-down or changed to 37ÂºC by adding hot YPD. These aliquots were cultured for 30 min and collected. Thus, wt and mutants have two samples: 30 and 37ÂºC. Each sample was done in triplicate.

2016-03-31 | E-GEOD-65283 | biostudies-arrayexpress

Genomic Run-On (GRO): determination of the nascent transcriptional rate and mRNA amount in Xrn1 mutants

Project description:Maintaining the proper mRNA levels is a key aspect in the regulation of gene expression. The balance between mRNA synthesis and decay determines these levels. Using a whole-genome analysis, we demonstrate that most yeast mRNAs are degraded by the 5'-to-3' pathway (the "decaysome"), as proposed previously. Unexpectedly, the level of these mRNAs is highly robust to perturbations in this major pathway, as defects in various decaysome components lead to transcription down-regulation. Moreover, these components shuttle between the cytoplasm and the nucleus, in a manner dependent on proper mRNA degradation. In the nucleus, they associate with chromatin - preferentially ~30bp upstream of transcription start-sites - and directly stimulate transcription initiation and elongation. Hence, the decaysome has a dual role in maintaining mRNA levels. Significantly, proper import of some decaysome components seems to play a key role in coupling the two functions. The gene expression process is therefore circular, whereby the hitherto first and last stages are interconnected. This study focuses on the transcriptional activity of RNA pol II in 6035 S. cerevisiae ORFs. S. cerevisiae cells grown in YPD to exponential phase were subjected to Genomic Run-On. Data were normalized using gDNA hybridized on the same array and by the software ArrayStat. Home-made macroarrays containing 6035 ORFs were used.

2013-05-22 | E-GEOD-29519 | biostudies-arrayexpress

Genomic Run On (GRO): determination of the nascent transcriptional rates and mRNA levels in several yeast mutants.

Project description:In order to maintain the appropriate level of mRNA it is necessary coordinate simultaneously all the steps along the mRNA life cycle. It has been shown that several factors act in the regulation of gene expression as global coordinators. Thus, some kind of information is transferred from the nucleus to the cytoplasm, imprinted in the mRNA. In this way, it is conceivable the existence of mechanisms that ensure the balance between mRNA synthesis and degradation through the information flow from the cytoplasm to the nucleus and vice versa, as a crosstalk among both process to ensure the proper mRNA homeostasis in the cell. In this study, we have used null mutants related with transcription and mRNA degradation and we find that the lack of those factors impacts both over transcription and RNA stability at genome wide levels to compensate the impaired effect produce by the loss of each studied factor. This study focus on the transcriptional activity of RNA pol II in yeast genes. S. cerevisiae cells grown in YPD or YPGal to exponential phase were subjected to Genomic Run On. Data were normalized by the ArrayStat software. Home-made macroarrays containing 6035 ORF were used.

2015-12-31 | E-GEOD-57467 | biostudies-arrayexpress

Genomic Run On (GRO): determination of the nascent transcriptional rates and mRNA levels in several yeast mutants (SAC3, SUS1, SRC1)

Project description:We analyzed the effect of SAC3, SUS1 and SRC1 on the transcription rates, mRNA stabilities and mRNA levels by doing GRO experiments in a deletion mutants and the partial C-truncated version of Sac3 comparing with a wild type. Some data for mRNA amounts (sus1 ans src1 mutants) are not included because were already in GEO database: GSE920 and GSE6370 accession numbers. This study focus on the transcriptional activity of RNA pol II in yeast genes. S. cerevisiae cells grown in YPD to exponential phase were subjected to Genomic Run On. Data were normalized by the ArrayStat software. Home-made macroarrays containing entire ORFs were used.

2015-12-31 | E-GEOD-63769 | biostudies-arrayexpress

Genomic Run On (GRO): determination of the nascent transcriptional rates in a series of a mex67 mutant.

Project description:The goal of the project was to check the effect on transcription rate of a sudden depletion of Mex67 protein by using a thermosensitive mutant: mex67-5 Cells were grown in YPD at 26ÂºC to 0.5 OD600. At that time cells were shifted to 37ÂºC to induce Mex67 protein inactivation and recovered after, 0, 5, 20, 40, 60 and 150 min.

2015-12-31 | E-GEOD-65228 | biostudies-arrayexpress

Distribution of elongating RNA polymerase II along the 5'/3' regions in xrn1 mutants

Project description:Determination of the 3' or 5' intragenic nascent transcriptional rate. Maintaining the proper mRNA levels is a key aspect in the regulation of gene expression. The balance between mRNA synthesis and decay determines these levels. Using a whole-genome analysis, we demonstrate that most yeast mRNAs are degraded by the 5'-to-3' pathway (the "decaysome"), as proposed previously. Unexpectedly, the level of these mRNAs is highly robust to perturbations in this major pathway, as defects in various decaysome components lead to transcription down-regulation. Moreover, these components shuttle between the cytoplasm and the nucleus, in a manner dependent on proper mRNA degradation. In the nucleus, they associate with chromatin - preferentially ~30bp upstream of transcription start-sites - and directly stimulate transcription initiation and elongation. Hence, the decaysome has a dual role in maintaining mRNA levels. Significantly, proper import of some decaysome components seems to play a key role in coupling the two functions. The gene expression process is therefore circular, whereby the hitherto first and last stages are interconnected. This study focuses on the transcriptional activity of RNA pol II in the 3' or 5' region of 377 S. cerevisiae ORFs. S. cerevisiae cells grown in YPD to exponential phase were subjected to Genomic Run-On. Data were normalized using gDNA hybridized on the same array. Home-made macroarrays containing 300 bp from both the 5' or 3' ends of each ORF were used.

2013-05-22 | E-GEOD-43602 | biostudies-arrayexpress

Genomic Run On (GRO): determination of the nascent transcriptional rates in a series of Hrp1 mutants.

Project description:The goal of the project was to check the differential effect on transcription rate of a sudden degron-induced depletion of Hpr1 protein and its comparison towards the effect of a constitutive absence of Hpr1 protein in a deletion strain. Cells were grown in YP-Raffinose + 0.1 mM CuSO4 at 26ÂºC to 0.5 OD600. At that cells were spun-down and changed to YP-Galactose without CuSO4 for 30 min at 26ÂºC. Then cells were shifted to 37ÂºC to induce degron-mediated proteolysis and recovered after 30 min. Samples include wt, hpr1delta and hpr1-degron after 0 or 30 min growth at 30ÂºC.

2015-12-31 | E-GEOD-65225 | biostudies-arrayexpress

Genomic Run On (GRO): determination of the nascent transcriptional rates and mRNA levels in several yeast mutants (PUB1 and NGR1)

Project description:We analyzed the effect of PUB1 and NGR1 on the transcription rates, mRNA stabilities and mRNA levels by doing GRO experiments in a deletion mutants comparing with a wild type in both glucose (YPD) and galactose (YPGal) media. Some data for the wt in YPGal are not included because were already in GEO database: GSE1002 accession number. This study focus on the transcriptional activity of RNA pol II in yeast genes. S. cerevisiae cells grown in YPD or YPGal to exponential phase were subjected to Genomic Run On. Data were normalized by the ArrayStat software. Home-made macroarrays containing 6035 ORF were used.

2015-12-31 | E-GEOD-63729 | biostudies-arrayexpress

Gene Expression Kinetics

Project description:We have taken five different time points of a Yeast culture in exponential grow in rich medium, each one elapsed ten minutes from de previous one (from OD600 0.36 to 0.47). Then, for each time point we have measured the transcription rates (TR) and mRNA amounts (RA) for all the genes using the Genomic run-on (GRO) technique . For each time point we have measured the transcription rates (GRO) with 3 replicates (except for the t2 that only has 2 replicates due to technical problems) and mRNA amounts (cDNA RP) with 3 replicates for all the genes. The data were normalized using a gDNA hybridization for each filter.

2010-03-05 | E-GEOD-11521 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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