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

SUR7 antisense disruption

ABSTRACT: Disruption of expression of SUR7 antisense in S. cerevisiae.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Charles Girardot

PROVIDER: E-TABM-1096 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Genotyping by array of yeast to map post-meiotic segregation across the yeast genome

Project description:To map post-meiotic segregation (PMS) across the yeast genome, we genotyped the two cells resulting from the first mitotic division of the four spores of 4 tetrads of a YJM789/S96 Saccharomyces cerevisiae hybrid strain. Sporulation was induced, tetrads were dissected, spores let to germinate and the two cells coming from the first mitotic division of each spore were finally dissected. DNA from each of the eight cells in each tetrad was extracted from independent overnight cultures in rich medium and hybridized to microarrays, one array per cell. Each hybridization was used to genotype the corresponding cell and genetic differences between the two cells from the same spore revealed PMS. Therefore there are 32 hybridization files, 2 per spore and 8 per tetrad.

2011-07-13 | E-TABM-1031 | biostudies-arrayexpress

Experimental relocation of the mitochondrial ATP9 gene to the nucleus reveals forces underlying mitochondrial genome evolution

Project description:Transcriptome profile of S. cerevisiae strains grown in rich ethanol/glycerol media, where the endogenous mitochondrial gene ATP9 has been deleted and relocated to the nucleus by expressing synthetic, codon-optimized versions of the Podospora anserina genes Atp9-5 and Atp9-7. The strains AMY7, AMY8, AMY10, and AMY11 each express one of these genes either from a centromeric or 2-micron plasmid. These strains are derived from RKY26, an atp9 deletion mutant which was not included in this experiment since it does not grow on respiratory media. The isogenic wild-type strain (MR6) was included as a control. Strains were produced for this study, and the arrays used were yeast tiling microarrays from Affymetrix. Note that normalization was performed using genomic DNA hybridizations, the raw data for which can be found in ArrayExpress Accession # E-TABM-1176.

2012-08-28 | E-MTAB-1115 | biostudies-arrayexpress

RNA profiling of rrp6 deletion in YPD

Project description:Transcription profiling was performed on 2 biological replicates of rrp6 deletion strains which were cultivated at 30C in YPAD medium and harvested at OD595~1

2013-04-18 | E-MTAB-1089 | biostudies-arrayexpress

Transcription profiling by array of Nab2 depletion effect on yeast mRNA

Project description:Transcription profiling was performed on the time course of Nab2 protein depletion in THC-Nab2 strain at 0h, 7h, 12h in biological triplicates to access its affect on the composition and structure of mRNA in budding yeast. For the protein depletion experiment THC-NAB2 (THJ collection Y2484, THC-NAB2:KAN tTA:URA, Open Biosystems) strain was used, where expression of the NAB2 gene is under control of a tetracyclin-repressible promoter.

2013-01-11 | E-MTAB-981 | biostudies-arrayexpress

A yeast-based assay identifies drugs active against human mitochondrial disorders

Project description:Transcriptome profile of S. cerevisiae strain MC6 (deletion mutant for the ATP synthase assembly factor FMC1, used as a yeast model of mitochondrial disease) grown at 35C in rich galactose media supplemented with either 1.25uM chlorhexidine (a drug identified in a yeast-based screen with potential therapeutic effects) or DMSO as a control. The isogenic wild-type strain (MC1) was included as a control. Strains originate from http://www.ncbi.nlm.nih.gov/pubmed/11096112 and the arrays used were yeast tiling microarrays from Affymetrix.

2011-07-01 | E-TABM-1176 | biostudies-arrayexpress

Loss of the yeast SR protein Npl3 alters gene expression due to transcription readthrough

Project description:Yeast Npl3 is a highly abundant RNA binding protein, related to metazoan SR proteins, with reported functions including transcription elongation, splicing and RNA 3’ end processing. To identify direct targets and functions for Npl3, we used UV crosslinking and analysis of cDNA (CRAC) to map precise RNA binding sites. Npl3 binds diverse RNA species, at sites indicative of roles in both early pre-mRNA processing and 3’ end formation on mRNAs and ncRNAs. Consistent with this, tiling array and RNAPII binding data revealed 3’ extended mRNA and snoRNA transcripts in the absence of Npl3. This reflected transcriptional readthrough by RNAPII, and extension and stabilization of cryptic unstable transcript (CUT) long noncoding RNAs. Transcription readthrough was widespread, often resulting in down-regulation of neighboring genes. We conclude that Npl3 is required for the formation of a termination-competent RNA, affecting both coding and noncoding RNAs.

2015-12-02 | E-MTAB-3642 | biostudies-arrayexpress

Transcription profiling by tiling array of Saccharomyces cerevisiae segregants spores obtained from a cross of the yeast strains S96 and YJM789.

Project description:Transcription profile in YPD media of 48 segregants spores obtained from a cross of the yeast strains S96 and YJM789. These spores are a subset of those published by Mancera et al, Nature, 2008. Two CEL files were mislabelled: eQTL_080822_spore_38B.CEL and eQTL_080826_spore_21C.CEL, actually spores 24A and 8D respectively. The correct spore IDs are in the sample annotation (under StrainOrLine).

2010-10-06 | E-TABM-845 | biostudies-arrayexpress

S.cerevisiae INO80 is required for promoter proximal nucleosome remodeling.

Project description:During transcription, nucleosomes are evicted from regulatory and coding regions yet chromatin structure is stable. Restoration of chromatin structure involves concerted action of chromatin modifying activities. Our analysis demonstrates a genome wide function of the INO80 remodeling complex for stable repositioning of the nucleosome immediately proximal to the transcription initiation site. INO80 dependent remodeling of the promoter proximal nucleosomes has a global repressive role. Recruitment of INO80 to proximal nucleosomes overlaps with the elongating Polymerase II complex assembly. The amount of associated Polymerase II at start sites correlates with INO80 recruitment for inducible and constantly transcribed genes. Furthermore, at highly inducible promoters INO80 is required for repression of bidirectional transcription. Therefore, we suggest a function for INO80 after transcription initiation to achieve Polymerase II dependent reassembly of promoter proximal nucleosomes.

2016-12-24 | E-MTAB-1810 | biostudies-arrayexpress

Road-block transcription termination by Reb1p enforces transcription boundaries

Project description:Widely transcribed and compact genomes face the major challenge of coping with frequent overlapping or concurrent transcription events. Efficient and timely transcription termination is crucial to control pervasive transcription. In yeast, RNA polymerase II (RNAPII) termination mainly occurs via two pathways, one generating mRNAs and one dedicated to non-coding RNAs, and is triggered by signals that are recognized on the nascent RNA by a specific complex. We describe here a novel pathway of RNAPII transcription termination that is triggered by the binding to the DNA of the transcriptional activator Reb1p. We show that termination follows road-block induced pausing of RNAPII and requires ubiquitylation of RNAPII. The released RNAs are rapidly degraded, which defines a new class of cryptic unstable transcripts. We show that Reb1p-dependent termination can prevent transcriptional interference. This work reveals a novel role for Reb1p and a new paradigm for preserving the functional integrity of nucleosome free regions.

2014-12-05 | E-MTAB-2241 | biostudies-arrayexpress

Temporal Expression Profiling Identifies Pathways Mediating Effect of Causal Variant on Phenotype

Project description:Temporal expression profiling during sporulation for MKT1 allele replacement strains in S288c

2015-04-18 | E-MTAB-3454 | biostudies-arrayexpress