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

Heat shock: genomic run-on (GRO) analysis

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE24483: TR heat-shock GSE24484: RA heat-shock Refer to individual Series

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Jose Perez-Ortin

PROVIDER: E-GEOD-24488 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Heat shock response in yeast involves changes in both transcription rates and mRNA stabilities.

Castells-Roca Laia L García-Martínez José J Moreno Joaquín J Herrero Enrique E Bellí Gemma G Pérez-Ortín José E JE

PloS one 20110225 2

We have analyzed the heat stress response in the yeast Saccharomyces cerevisiae by determining mRNA levels and transcription rates for the whole transcriptome after a shift from 25 °C to 37 °C. Using an established mathematical algorithm, theoretical mRNA decay rates have also been calculated from the experimental data. We have verified the mathematical predictions for selected genes by determining their mRNA decay rates at different times during heat stress response using the regulatable tetO p ...[more]

PMID: 21364882

Similar Datasets

TR heat-shock

Project description:Within a GRO experiment, samples for Transcription rate (TR) analysis were taken at 0, 4, 11, 16, 26 and 40 minutes after heat stress (from 25ºC to 37ºC) and subjected to run-on. Analysis was done in filters also used for RA analysis of aliquots from the same cultures. The analysis includes 3 repeats of stress treatment of the W3030-1a strain. The same times were used for sampling in each repeat of the experiment. A single genomic DNA hybridization on every one of the filters is used for normalization between gene probes.

2011-04-19 | E-GEOD-24483 | biostudies-arrayexpress

RA heat-shock

Project description:Within a GRO experiment, samples for mRNA amount (RA) were taken at 0, 4, 11, 16, 26 and 40 minutes after heat stress (from 25ºC to 37ºC). Analysis was done in filters also used for Transcription rate (TR) analysis of aliquots from the same cultures. The analysis includes 3 repeats of stress treatment of the W3030-1a strain. The same times were used for sampling in each repeat of the experiment. A single genomic DNA hybridization on every one of the filters is used for normalization between gene probes.

2011-04-19 | E-GEOD-24484 | 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

mRNA amount analysis of W303 hog1 mutant strain subjected to osmotic stress

Project description:mRNA amount (RA) analysis of W303 hog1 mutant yeast strain growing in exponential phase in YPD subjected to osmotic stress Keywords: Time course Transcriptomic analysis 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-13099 | 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

mRNA amount analysis of wild type strain subjected to osmotic stress

Project description:mRNA amount (RA) analysis of W303-1a yeast strain growing in exponential phase in YPD subjected to osmotic stress Keywords: time course Transcriptomic analysis 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-13097 | biostudies-arrayexpress

Topo mutants psoralen photobinding

Project description:We present a DNA array-based method for the genome-wide analysis of Psoralen photobinding in Saccharomyces cerevisiae cells. PB was found reduced in subtelomeric regions and increased in the subset of genes with smallest nucleosomal density. The analysis includes 3 repeats of the wild type strain (JCW25) at 30ÂºC and 3 more at 37ÂºC, 3 repeats of the double top1 (delta) top2ts mutant at 37ÂºC and 3 repeats of naked genomic DNA treated with trimethyl psoralen (TMP) in the same way to be used as a control of unspecific binding.

2010-06-24 | E-GEOD-16758 | biostudies-arrayexpress

GRO analysis of topoisomerase mutants

Project description:Genomic Run-on analysis of topoisomerase mutants (top1-delta/top2ts or top2ts) has been conducted at reference temperature for wt strain and at non-permissive temperature for wt and mutant strains. Keywords: Genomic Run On The analysis includes 3 repeats of the wild type strain (JCW25) at 30ÂºC and 3 more at 37ÂºC, 3 repeats of the top2ts mutant (JCW26) at 37ÂºC and 3 repeats of the double top1 (delta) top2ts mutant at 37ÂºC. A single genomic DNA hybridization on one of the filters can be used for normalization between gene probes if needed.

2010-06-24 | E-GEOD-16673 | biostudies-arrayexpress

RNA pol II ChIP on chip (RPCC)

Project description:Adaptation of the ChIP-on-chip protocol, to calculate genomic transcription rates in S. cerevisiae. Keywords: ChIP-chip There are 3 different experimental conditions: -Yeast cell growing exponentially in YPD. -Yeast cell stopped after 2 h of changing them to YPGal. -Yeast cell growing exponentially after 14.5 h of changing them to YPGal. We have used 3 different IP protocols: -total RNApol II using a Myc tagged RNApol (RPB1-Myc) -RNApol II CTD using the Ab 8WG16 (Covance) -RNApol II CTD Phosphorilated on Ser5 (David Bentley\'s lab) There are 3 independent biological replicates of each experiment.

2010-06-24 | E-GEOD-14060 | 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