Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Inferring the stress-activated signaling network in yeast through multi-omic data integration

ABSTRACT: Transcriptome profiling of yeast mutant strains responding to 0.7M NaCl treatment for 30 minutes. This study identified affected genes in each mutant and used it to computationally infer the complete NaCl-activated signaling network in yeast.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE51844 | GEO | 2014/12/03

SECONDARY ACCESSION(S): PRJNA225621

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Inferring the stress-activated signaling network in yeast through multi-omic data integration

Project description:Transcriptome profiling of yeast mutant strains responding to 0.7M NaCl treatment for 30 minutes. This study identified affected genes in each mutant and used it to computationally infer the complete NaCl-activated signaling network in yeast. Two-color fluorescence arrays reporting on mRNA abundance in strains before and at 30 min after a shock with 0.7M NaCl, hybridized to yeast tile-genome Nimblegen arrays

2014-12-03 | E-GEOD-51844 | biostudies-arrayexpress

NeuCode metabolic labeling reveals a high correlation between mRNA and protein abundance during salt adaptation in S. cerevisiae.

2013-12-21 | GSE53549 | GEO

NeuCode metabolic labeling reveals a high correlation between mRNA and protein abundance during salt adaptation in S. cerevisiae.

Project description:Transcriptome profiling of yeast strains responding to 0.7M NaCl treatment for 30 or 60 minutes. This study identified affected genes under both conditions tested. Transcript and protein changes were compared to determine mRNAs contribution to protein levels during salt acclimation. Two-color fluorescence arrays reporting on mRNA abunance in strains before and at 30 min or 60 min after a shock with 0.7M NaCl, hybridized to yeast tile-genome Nimblegen arrays

2013-12-21 | E-GEOD-53549 | biostudies-arrayexpress

Multiple means to the same end: The genetic basis of acquired stress resistance in yeast

2014-03-06 | GSE27819 | GEO

Saccharomyces cerevisiae response to various stressors

Project description:Samples GSM206658-GSM206693: Acquired Stress resistance in S. cerevisiae: NaCl primary and H2O2 secondary Transcriptional timecourses of yeast cells exposed to 0.7M NaCl alone, 0.5mM H2O2 alone, or 0.5mM H2O2 following 0.7M NaCl, all compared to an unstressed sample. Repeated using msn2∆ strain. Samples GSM291156-GSM291196: Transcriptional response to stress in strains lacking MSN2 and/or MSN4 Transcriptional timecourses of yeast cells (WT, msn2∆, msn4∆, or msn2∆msn4∆) exposed to 0.7M NaCl for 45 minutes or 30-37˚C Heat Shift for 15 min compared to an unstressed sample of the same strain. Keywords: Stress Response

2008-09-05 | GSE8335 | GEO

Multiple means to the same end: The genetic basis of acquired stress resistance in yeast

Project description:A series of experiments comparing the gene expression response before and after 30 min 0.7M NaCl exposure in WT and mutant yeast strains. Mutant strains were identified as having a defect in acquiring resistance to H2O2 following mild NaCl pretreatment. The mutants in this study were taken from the Yeast Knock-Out Collection, mat a. Unstressed cells vs cells exposed to 0.7M NaCl for 30 min; 5 replicates for WT, 3 replicates for hog1∆, msn2∆, mck1∆, pde2∆, rim101∆, and 2 replicates for the remaining mutants.

2014-03-06 | E-GEOD-27819 | biostudies-arrayexpress

nup42-delta cells pretreated with NaCl lose the altered gene expression in response to H2O2

Project description:BY4741 (S288c haploid) cells have different gene expression in response to 0.4mM H2O2 when pretreated with 0.7M NaCl compared to cells that are not pretreated with NaCl (mock cells). Cells lacking Nup42p do not exhibit a different gene expression in response to H2O2 between naive cells and cells pretreated with 0.7M NaCl

2011-09-18 | GSE32196 | GEO

Modification of C-terminal Domain (CTD) of RPB1 plays a role in transcriptome change upon salt stress

Project description:Transctriptome profiling of CTD-14 repeats, 2A, 5A mutants responding to 0.7N NaCl for 30mins. The study shows that phosphorylation at Ser5 sites plays a role in normal induction and repression of genes upon NaCl stress. The CTD14 strains harbors a plasmid expressing RPB1 with 14 wild-type CTD repeats. 5A strains carries a plasmid expressing a chimeric RPB1 in which the CTD was composed of 5 repeats of CTD-serine 5 substituted with Ala followed by 7 wild-type-sequenced repeats. The 2A strains carrys 8 repeats of CTD-serine 2 substituted with alanine followed by 7 wild-type-sequenced repeats. Two-color fluorescence arrays reporting on mRNA abunance in strains before and after 30 min with 0.7M NaCl treatment

2014-12-03 | E-GEOD-60700 | biostudies-arrayexpress

Inferring secretory and metabolic pathway activity from omic data with secCellFie

Project description:Understanding protein secretion has considerable importance in the biotechnology industry and important implications in a broad range of normal and pathological conditions including development, immunology, and tissue function. While great progress has been made in studying individual proteins in the secretory pathway, measuring and quantifying mechanistic changes in the pathway's activity remains challenging due to the complexity of the biomolecular systems involved. Systems biology has begun to address this issue with the development of algorithmic tools for analyzing biological pathways; however most of these tools remain accessible only to experts in systems biology with extensive computational experience. Here, we expand upon the user-friendly CellFie tool which quantifies metabolic activity from omic data to include secretory pathway functions, allowing any scientist to infer protein secretion capabilities from omic data. We demonstrate how the secretory expansion of CellFie (secCellFie) can be used to predict metabolic and secretory functions across diverse immune cells, hepatokine secretion in a cell model of NAFLD, and antibody production in Chinese Hamster Ovary cells.

2024-06-20 | GSE248376 | GEO

Natural variation in the consequences of gene overexpression during osmotic stress [RNA-Seq]

Project description:We used RNA-Seq to measure transcript abundance in 4 Saccharomyces cerevisiae strains (BY4743, BC187, NCYC3290, and YPS128) from a diverse range of genetic lineages when growing in rich media (YPD) with 0.7M NaCl to characterize differential expression across strains in response to osmotic and ionic stress.

2023-06-30 | GSE226246 | GEO

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