Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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).

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Charles Girardot

PROVIDER: E-TABM-590 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of yeast laboratory strain S288c and clinical isolate YJM789 and a heterozygous hybrid strain to profile allele- and strand-specific expression

Project description:To profile genome-wide allele-specific expression in an unbiased manner we designed a high-resolution yeast tiling microarray that covers the genomes of both the laboratory strain S288c and the recently sequenced clinical isolate YJM789. This array design allows simultaneous expression profiling of allelic variants in a heterozygous hybrid strain. We hybridized cDNA from the heterozygous Y/S and from the homozygous S and Y strains grown in rich medium (YPD). Strand specificity during sample preparation was maintained by inclusion of actinomycin D during reverse transcription to prevent spurious synthesis of second strand cDNA.

2009-02-10 | E-TABM-569 | biostudies-arrayexpress

Transcription profiling of yeast SEN1 mutant versus wildtype

Project description:Transcription profiling of yeast SEN1 mutant versus wild-type

2010-11-27 | E-TABM-863 | 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

Transcription profiling by tiling array of yeast ssu72, rrp6, and rco1 mutants

Project description:Genome-wide analysis of ssu72 and rrp6 mutants in Yeast

2011-05-03 | E-TABM-936 | 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

Investigating the role of a coding polymorphism in TAO3 in sporulation efficiency variation in yeast

Project description:Temporal expression profiling during sporulation for TAO3(4477C) allele replacement strains in S288c. Raw gene expression data CEL files for control TAO3(4477G) allele strain are given in E-MTAB-3454 (see 9 array files from \S_Spo0h0m_Scerevisiae_tlg.CEL\ to \S_Spo8h30m_Scerevisiae_tlg.CEL\).

2015-12-31 | E-MTAB-3889 | 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

Tiling path analysis of Saccharomyces cerevisiae reveals a genome-wide role for the SAS-I histone acetyltransferase in transcription elongation and suppression of cryptic initiation

Project description:Genome-wide analysis of SAS-I-mediated H4 K16 acetylation

2011-01-26 | E-TABM-901 | 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 of yeast using samples prepared with actinomycin D to exclude antisense artifacts

Project description:Recent transcription profiling studies have revealed an unanticipatedly large proportion of antisense transcription across eukaryotic and bacterial genomes. However, the extent and significance of antisense transcripts is controversial partly because experimental artifacts are suspected. Here, we present a method to generate clean genome-wide transcriptome profiles, using actinomycin D (ActD) during reverse transcription. We show that antisense artifacts appear to be triggered by spurious synthesis of second-strand cDNA during reverse transcription reactions. Strand-specific hybridization signals obtained from Saccharomyces cerevisiae tiling arrays were compared between samples prepared with and without ActD. Use of ActD removed about half of the detectable antisense transcripts, consistent with their being artifacts, while sense expression levels and about 200 antisense transcripts were not affected. Our findings thus facilitate a more accurate assessment of the extent and position of antisense transcription, towards a better understanding of its role in cells.

2007-10-30 | E-TABM-361 | 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