Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

51 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

YPD to YPGal timecourse

ABSTRACT: Timecourse analyses (0 to 850 min) of exponentially growing BQS252 yeast after shift from YPD to YPGal galactose medium. Total RNA in vivo labeled by run-on, or cDNA labelling using random decamers included. Genomic DNA also examined. Keywords: other

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Jose Perez-Ortin

PROVIDER: E-GEOD-1002 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms.

García-Martínez José J Aranda Agustín A Pérez-Ortín José E JE

Molecular cell 20040701 2

Most studies of eukaryotic gene regulation have been done looking at mature mRNA levels. Nevertheless, the steady-state mRNA level is the result of two opposing factors: transcription rate (TR) and mRNA degradation. Both can be important points to regulate gene expression. Here we show a new method that combines the use of nylon macroarrays and in vivo radioactive labeling of nascent RNA to quantify TRs, mRNA levels, and mRNA stabilities for all the S. cerevisiae genes. We found that during the ...[more]

PMID: 15260981

Similar Datasets

Gene category-specific regulation of transcription elongation across the yeast genome

Project description:Analysis of genome-wide differences of transcription using Genomic run-on (GRO), RNApol II ChIP-on-Chip, cDNA analysis and ChIP-on-Chip. This SuperSeries is composed of the following subset Series: GSE14060 RNA pol II ChIP on chip (RPCC) GSE14077 RPCC analysis of rap1-sil, tpk1 & tpk2 GSE14080 GRO analysis of rap1-sil, tpk1 & tpk2 GSE14082 Analysis of Spt16 depletion GSE1002 YPD to YPGal timecourse Refer to individual Series

2010-06-24 | E-GEOD-14084 | biostudies-arrayexpress

Normal, sluggish and recovered fermentation

Project description:Gene expression analysis of time course experiment of [1] a synthetic must (nitrogen-rich) fermentation by a natural wine yeast; [2] a synthetic must (nitrogen-poor) fermentation by a natural wine yeast; and [3] a synthetic must (nitrogen-poor) fermentation by a natural wine yeast, supplemented at 72 hours with 200 mg/l of nitrogen. This SuperSeries is composed of the following subset Series: GSE5835: Normal Fermentation GSE5836: Sluggish Fermentation GSE5837: Recovered Fermentation Keywords: SuperSeries Refer to individual Series, and to genomic hybridization of the individual membranes used for normalizing single samples.

2010-07-01 | E-GEOD-5842 | biostudies-arrayexpress

Sluggish Fermentation

Project description:Gene expression analysis of a time course experiment of a synthetic must (nitrogen-poor) fermentation by a natural wine yeast. Three replicates of five time points taken at 24, 48, 80, 96 and 144 hours after yeast inoculation

2010-07-01 | E-GEOD-5836 | biostudies-arrayexpress

Recovered Fermentation

Project description:Gene expression analysis of a time course experiment of a synthetic must (nitrogen-poor) fermentation by a natural wine yeast, supplemented at 72 hours with 200 mg/l of nitrogen Three replicates of five time points taken at 24, 48, 80, 96 and 144 hours after yeast inoculation. Time points 24 and 48 hours are common to Sluggish fermentation. Time points at 80, 96 and 144 hours are exclusive of this experiment.

2010-07-01 | E-GEOD-5837 | biostudies-arrayexpress

Osmotic stress on yeast S. cerevisiae

Project description:mRNA amount (RA) and Transcription rate (TR) analysis of W303-1a (wt) and hog1 mutant yeast strains growing in exponential phase in YPD subjected to osmotic stress This SuperSeries is composed of the following subset Series: GSE13096: Transcription rate analysis of wild type strain subjected to osmotic stress GSE13097: mRNA amount analysis of wild type strain subjected to osmotic stress GSE13098: Transcription rate analysis of W303 hog1 mutant strain subjected to osmotic stress GSE13099: mRNA amount analysis of W303 hog1 mutant strain subjected to osmotic stress Refer to individual Series Transcriptomic and transcription rate analysis by means of GRO of three independent replicates the yeast strain growing in exponential phase. Each time point replicate has been hybridized on a different macroarray (F11-F24). A single DNA genomic hybridization from the same labeling reaction was done on the same microarrays for normalization.

2010-06-19 | E-GEOD-13100 | biostudies-arrayexpress

Transcription rate analysis of wild type strain subjected to osmotic stress

Project description:Transcription rate (TR) analysis of W303-1a yeast strain growing in exponential phase in YPD subjected to osmotic stress Keywords: time course Transcription rate analysis by means of GRO of three independent replicates the yeast strain growing in exponential phase. Each time point replicate has been hybridized on a different macroarray (F11-F17).

2010-06-19 | E-GEOD-13096 | biostudies-arrayexpress

Transcription rate analysis of W303 hog1 mutant strain subjected to osmotic stress

Project description:Transcription rate (TR) analysis of W303 hog1 mutant yeast strain growing in exponential phase in YPD subjected to osmotic stress Keywords: Time course Transcription rate analysis by means of GRO of three independent replicates the yeast strain growing in exponential phase. Each time point replicate has been hybridized on a different macroarray (F18-F24).

2010-06-19 | E-GEOD-13098 | biostudies-arrayexpress

Terbutyl stress TR

Project description:Transcription rate (TR) analysis of W303-1a yeast strain growing in exponential phase in YPD subjected to terbutyl stress Keywords: time course Transcription rate analysis by means of GRO of three independent replicates the yeast strain growing in exponential phase. Each time point replicate has been hybridized on a different macroarray (F5-F10). A single DNA genomic hybridization from the same labeling reaction was done on the same macroarrays for normalization.

2008-05-23 | E-GEOD-9663 | biostudies-arrayexpress

Normal Fermentation

Project description:Gene expression analysis of a time course experiment of a synthetic must (nitrogen-rich) fermentation by a natural wine yeast. Three replicates of three time points taken at 24, 48 and 96 hours after yeast inoculation

2010-07-01 | E-GEOD-5835 | 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