Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

31 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Environmentally persistent genetic associations with gene expression reveal pathways mediating genetic signals to phenotype

ABSTRACT: Unraveling the causal chain of biochemical events that link genotype to phenotype is critical for understanding the molecular basis of genetic diseases and for designing personalized drug therapies. To this end, using yeast as a model system, we carried out joint profiling of fitness and gene expression. Transcription profile includes 4 media (YPD (YPE, YPMalt, YPE and YPD_BPS) of ~35 segregants spores each media were 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. Sufficient cells were grown at 30 °C in media of interest to the mid log phase. After harvest, gene expression profiling were performed using tiling array as previous described (Xu et al, Nature, 2009). The expression level of each transcript was used as molecular trait for further investigation in the study. 1 CEL data files was mislabelled: 110427_09C_BPS_(Scerevisiae_tlg).CEL.gz, actually spores 09D. The correct spore IDs are in the sample annotation (under StrainOrLine or sample name).

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Chenchen Zhu

PROVIDER: E-MTAB-1398 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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 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

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

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

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

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

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

3' isoform specific RNA IP (3' isRIP-seq) for PUF3 RBP in budding yeast

Project description:Exponentially growing cells (OD 0.5-0.8) from the TAP-tagged strain were harvested by ultracentrifugation followed by of washing and flash freezing in liquid nitrogen and breakage in FastPrep24 (ZYmoresearch S6005). The lysate was subjected to IP with Dyna M280 sheep anti rabbit IgG beads for 2h at 4C. An aliquot was taken before the IP as an input control. The IP of the RNA-protein complex was subjected to cleavage by TEV protease to cleave the TAP-tag off the protein. The bound RNA was then precipitated in phenol/chloroform/isoamyl-alcohol and sequenced using 3' T-filling protocol as described by Wilkening et al 2013 to obtain accurate quantification of 3' isoforms. We used the R Bioconductor package DESeq2 (Anders and Huber 2010) to call for differential log change between the Input and the RNA-IP sample and took all those isoforms as differentially regulated which had more than 4-fold change at a FDR of 10% as reported by the package.

2014-11-13 | E-MTAB-2103 | 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