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Genomic Run-On (GRO) experiment for the YPD to YPGal time course

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

PROVIDER: GSE1002 | GEO | 2004/07/29

SECONDARY ACCESSION(S): PRJNA114293

REPOSITORIES: GEO

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YPD to YPGal timecourse

Project description: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

2004-07-29 | E-GEOD-1002 | biostudies-arrayexpress

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

2015-12-31 | GSE63729 | GEO

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

Saccharomyces cerevisiae Transcript Isoform mapping

Project description:Extensive transcriptional heterogeneity revealed by isoform profiling Application of TIF-Seq (Transcript IsoForm Sequencing) to S.cerevisiae. The method was applied to simultaneously identify the 5' capped mRNA transcription start site and the 3' polyadenylation site in different conditions: WT cells grown in glucose media [ypd, 2 biological replicates (bio) and 3 independent library preparations, technical replicates(lib)], WT cells grown in galactose media [ypgal, 4 biological replicates (bio) and 3 independent library preparations, technical replicates(lib)]. A modified protocol designed to enrich in long mRNA molecules was performed for WT cells grown in glucose media [ypd, 2 biological replicates (bio)] and in galactose media [ypgal, 2 biological replicates (bio)] conditions. Finally, control samples performed with a modified protocol designed to identify non-capped but polyadenylated molecules was performed in WT cells grown both in glucose (nypd) and galactose (nypgal) media.

2013-05-06 | E-GEOD-39128 | 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

Transcription profiling of wild type yeast grown in synthetic complete or rich media with glucose, galactose, or ethanol (YPD, YPE, YPGal and SC) to identify strand-specific transcript levels and positional information.

Project description:This experiment was performed to obtain strand-specific transcriptional profiles of haploid yeast in four different growth conditions. This helps to better understand how sense and antisense transcription changes as a function of growth condition and thus complements the protein-based data of the publication this dataset refers to.Haploid yeast (strain YMaM330) were grown to mid-log phase in one of 4 growth media: rich media with either glucose, galactose or ethanol (YPD, YPGal or YPE) as carbon sources or synthetic growth medium with glucose as a carbon source (SC). Strand-specific tiling arrays were then used to measure RNA levels of both coding and non-coding transcripts. We found the transcriptome to be very similar to diploid yeast and therefore used the annotation established in Xu Z., Nature, 2009. The expression profiles are available in a searchable web-database (http://steinmetzlab.embl.de//cgi-bin/viewKnopLabArray.pl?showSamples=KnopHaploidTest2&type=heatmap).

2016-05-16 | E-MTAB-4731 | 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

Transcription profiling of wild type yeast grown with ethanol, glucose and galactose and the deletion mutant of Rrp6 to identify transcription start and end positions

Project description:To obtain a comprehensive survey of the structure and expression level of transcripts across the yeast genome, we used tiling arrays to profile wild-type transcriptomes in ethanol (YPE), glucose (YPD, SDC), and galactose (YPGal), which together encompass the main laboratory growth conditions of yeast. Transcript start and end positions were mapped to the genome by a segmentation algorithm and subsequent manual curation. To identify Cryptic Unstable Transcripts (CUTs), profiles were also measured for a deletion mutant of Rrp6, an important component of the nuclear exosome, which is involved in the degradation of CUTs. Expression profiles are provided in a searchable web-database (http://steinmetzlab.embl.de/NFRsharing).

2008-11-26 | E-TABM-590 | biostudies-arrayexpress

Depletion and reconstitution of 5S RNP complexes in early pre60S ribosomes

Project description:We purified pre60S ribosomes from yeast using Nsa1-FtpA as bait in Tandem Affinity Purification experiments. We tested the depletion of RPF2, using a Galactose-depletion system, to obtain ribosomal particles depleted of 5S RNP complexes. Sample A1: Control group (wild type strain) grown in YPGal; Sample A2: Control group (wild type strain) grown in YPGlu; Sample A3: Control group (Gal::HA-RPF2 strain) grown in YPGal; and Sample A4: Test group (Gal::HA-RPF2) shifted from YPGal to YPGlu for 6 hours to achieve 5S RNP depletion. Sample N1: Purified pre-60S Nsa1-associated with 5S RNP depleted after Sucrose gradient separation; Sample N2: Purified pre-60S Nsa1-associated with 5S RNP reconstituted after Sucrose gradient separation.

2023-10-24 | PXD040306 | Pride

Saccharomyces cerevisiae 3' poly(A) site mapping

Project description:The use of alternative polyadenylation sites is common and affects the post-transcriptional fate of mRNA, including its stability, localization, and translation. Here we present a method for genome-wide and strand-specific mapping of poly(A) sites and quantification of RNA levels at unprecedented efficiency by using an on-cluster dark T-fill procedure on the Illumina sequencing platform. Our method outperforms former protocols in quality and throughput, and reveals new insights into polyadenylation in Saccharomyces cerevisiae. Experimental benchmark of five different protocols (3tfill, bpmI, internal, rnaseq and yoon) for genome-wide identification of polyadenylation sites in Saccharomyces cerevisiae and transcript quantification. RNA was extracted from WT cells grown in glucose (ypd) or galactose (ypgal) as carbon source. The same RNA was used for 3 independent library constructions (technical replicates, rep).

2013-01-10 | E-GEOD-40110 | biostudies-arrayexpress

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