Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

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

INSTRUMENT(S): GeneChip 3000 7G

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Himanshu Sinha

PROVIDER: E-MTAB-3454 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

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

Project description: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).

2013-08-12 | E-MTAB-1398 | biostudies-arrayexpress

Expression-profiling of the Mediator transcription complex

Project description:Proteins from within the Saccharomyces cerevisiae Mediator transcription complex were knocked out and compared against wild type yeast using two-color oligo arrays.

2005-08-15 | E-UMCU-20 | 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

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

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 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 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

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