Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Topo mutants psoralen photobinding

ABSTRACT: 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.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Jose Perez-Ortin

PROVIDER: E-GEOD-16758 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

Analysis of Spt16 depletion

Project description: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.

2010-06-24 | E-GEOD-14082 | 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

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

RPCC analysis of rap1-sil, tpk1 & tpk2.

Project description:RPCC (RNA pol II ChIP-on-chip) experiments with different mutants that affect to the accumulation of non active RNA pol II along the yeast genome. Keywords: ChIP-chip 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). The IP was done using an Ab against the RNApol II CTD (8WG16 Covance).There are 3 independent biological replicates of Rap1 and rap1-sil experiments and 2 for the tpk1 & tpk2 experiments.

2010-06-24 | E-GEOD-14077 | biostudies-arrayexpress

ChIP-chip of Spo14 and Mvp1

Project description:Genome-wide localization of two new RNA pol II interacting proteins. We use C-LYTAG to map binding sites of Spo14 and Mvp1 along the S. cerevisiae genome. Two biological replicates of each experiment were done. Keywords: ChIp-chip Two independent biological replicates of each IP. We used three macroarrays: V5R2-L1-20, V5R2-L1-21 and V5R2-L1-22 that were hybridized with Whole Cell Extract (WCE) and then with two biological samples of immunoprecipitated (IP) Mvp1 (V5R2-L1-20 and V5R2-L1-21) and Spo14 (V5R2-L1-20 and V5R2-L1-22)

2011-10-31 | E-GEOD-16905 | 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

Heat shock: genomic run-on (GRO) analysis

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

2011-04-19 | E-GEOD-24488 | 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

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

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