Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

58 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis of Spt16 depletion

ABSTRACT: Transcription rate analysis in Yeast by means of GRO, mRNA amount and ChIP-on-chip during the depletion of Spt16p. Keywords: Genomic run-on GRO ChIP-chip Transcription rate analysis by means of GRO and mRNA amount (RA) of three independent replicates during the depletion of Spt16p (Control and 5 & 7 hours after the depletion). Each time point replicate has been hybridized on a different macroarray (F14-F16). ChIP-on-chip analysis of Spt16 were done during exponential grow in YPD.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Jose Garcia-Martinez

PROVIDER: E-GEOD-14082 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Regulon-specific control of transcription elongation across the yeast genome.

Pelechano Vicent V Jimeno-González Silvia S Rodríguez-Gil Alfonso A García-Martínez José J Pérez-Ortín José E JE Chávez Sebastián S

PLoS genetics 20090821 8

Transcription elongation by RNA polymerase II was often considered an invariant non-regulated process. However, genome-wide studies have shown that transcriptional pausing during elongation is a frequent phenomenon in tightly-regulated metazoan genes. Using a combination of ChIP-on-chip and genomic run-on approaches, we found that the proportion of transcriptionally active RNA polymerase II (active versus total) present throughout the yeast genome is characteristic of some functional gene classe ...[more]

PMID: 19696888

Similar Datasets

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

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

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

GRO analysis of rap1-sil, tpk1 & tpk2.

Project description:GRO (Genomic run-on) experiments with different mutants that affect to the accumulation of non active RNA pol II along the yeast genome. Keywords: Genomic run-on GRO There are 4 different strains: rap1-sil (without the silencing domain), RAP1(both from Graham I.R. et al 1999) and tpk1 & tpk2 mutants (Euroscarf). For each experiment there are GRO data (Transcription Rate) and gDNA data used for normalizing the GRO signals. The last number of the GRO filters correspond to the number of gDNA filters.There are 3 independent biological replicates of Rap1 and rap1-sil experiments and 2 for the tpk1 & tpk2 experiments.

2010-06-24 | E-GEOD-14080 | 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

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

Yeast mRNA decay analysis after addition of 3 Âµ/mL thiolutin

Project description:Time course after the addition of the transcriptional inhibitor thiolutin at 3Âµg/mL to an exponential growing culture of S. cerevisiae in YPD. Total RNA from BQS252 yeast strain (Mat a, ura 3-52 derived from FY1679) growing in exponential phase in YPD was extracted at different times after thiolutin 3Âµg/mL addition. All the samples were hybridized on the same nylon array. In order to estimate mRNA stability the intensities where normalized using global poly(A) data from a RNA dot-blot and assuming a first order decaying. There is only 1 replicate.

2010-06-25 | E-GEOD-7261 | biostudies-arrayexpress

Yeast mRNA decay analysis after addition of 3 & 10 Âµ/mL thiolutin

Project description:Time course after the addition of the transcriptional inhibitor thiolutin at 3 and 10 Âµg/mL to an exponential growing culture of S. cerevisiae in YPD. Total RNA from BQS252 yeast strain (Mat a, ura3-52 derived from FY1679) growing in exponential phase in YPD was extracted at 30 minutes after thiolutin 3 and 10 Âµg/mL addition. All the samples were hybridized on the same nylon array. 2 replicates.

2010-06-25 | E-GEOD-8629 | 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