Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A multi-omics dataset of heat-shock response in the yeast RNA transport protein Mip6

ABSTRACT: A multi-omics dataset of heat-shock response in the yeast RNA transport protein Mip6

PROVIDER: PRJNA559331 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

A multi-omics dataset of heat-shock response in the yeast RNA transport protein Mip6

Project description:We studied the heat-shock response in wild-type (wt) and in absence of Mip6, an RNA binding protein with roles at multiple levels of the gene expression pathway. This study include; their transcriptome (RNA-seq), metabolome (targeted NMR) and H4K12ac epigenome (ChIP-seq) using an experimental desing that ensures that the same samples are used across all omics determinations. This facilitates data analysis approaches that can leverage fully matched, longitudinal, replicated data. These data will faciliate studies of covariation patterns across multiple molecular layers controlling and responding to RNA biogenesis.

2019-11-21 | GSE135568 | GEO

A multi-omics dataset of heat-shock response in the yeast RNA binding protein Mip6 (NMR assay)

Project description:<p>Gene expression is a biological process regulated at different molecular levels, including chromatin accessibility, transcription, and RNA maturation and transport. In addition, these regulatory mechanisms have strong links with cellular metabolism. Here we present a multi-omics dataset that captures different aspects of this multi-layered process in yeast. We obtained RNA-seq, metabolomics, and H4K12Ac ChIP-seq data for wild-type and mip6delta strains during a heat-shock time course. Mip6 is an RNA-binding protein that contributes to RNA export during environmental stress and is informative of the contribution of post-transcriptional regulation to control cellular adaptations to environmental changes. The experiment was performed in quadruplicate, and the different omics measurements were obtained from the same biological samples, which facilitates the integration and analysis of data using covariance-based methods. We validate our dataset by showing that ChIP-seq, RNA-seq and metabolomics signals recapitulate existing knowledge about the response of ribosomal genes and the contribution of trehalose metabolism to heat stress.</p>

2020-02-14 | MTBLS1320 | MetaboLights

A multi-omics dataset of heat-shock response in the yeast RNA binding protein Mip6.

Project description: Not available

| S-EPMC7046740 | biostudies-literature

Multi-layer omics dataset for cross-species translational systems biology

Project description:Inferring in humans biological responses to external cues such as drugs, chemicals, viruses and hormones, is an essential question in biomedicine and cannot be easily studied in humans. Thus, biomedical research has continuously relied on animal models for studying the impact of these compounds and attempted to M-^StranslateM-^T the results to humans. In this context, the Systems Biology Verification for Industrial Methodology for Process Verification in Research (SBV IMPROVER) initiative had run a Species Translation Challenge for the scientific community to explore and understand the limit of translatability from rodent to human using systems biology. Therefore, a multi-layer omics dataset was generated that comprised of phosphoproteomics, transcriptomics and cytokine data derived from normal human (NHBE) and rat (NRBE) bronchial epithelial cells exposed in parallel to more than 50 different stimuli under identical conditions. The present manuscript describes in detail the experimental settings, the generation, processing and quality control analysis of the multi-layer omics dataset. The datasets are accessible in public repositories could be leveraged for further translation studies.

2014-06-10 | E-MTAB-2091 | biostudies-arrayexpress

Heat shock stimulates genomic instability and phenotypic variations in yeast

Project description:Yeast Saccharomyces cerevisiae has been widely used as a model system for studying genomic instability. In this study, heat-shock-induced genomic alterations were explored in the heterozygous diploid yeast strain JSC25-1. In combination of the whole-genome microarray, the patterns of chromosomal instability induced by heat shock could also be explored at a whole genome level. Using this system, we found heat-shock treatment resulted in hundreds-fold higher rate of genomic alterations, including aneuploidy and loss of heterozygosity (LOH).

2020-05-18 | GSE150711 | GEO

Genomics of the individual heat shock response

Project description:The transcriptional response to heat shock is essential for cells to function effectively under stress. This is a highly heritable trait but the nature and extent of inter-individual variation in heat shock response are not well established. This dataset consists of the global transcription profiles for a panel of lymphoblastoid cell lines established from 60 founder individuals in the Yoruba HapMap population that have been exposed to heat shock. RNA was extracted from resting cells as well as cells that were exposed to heat shock at 42Â°C for 1 hour and then allowed to recover for 6 hours at 37Â°C. In combination with the HapMap genotypes for these individuals this enables the study of the effect of genetic variation on the heat shock response.

2016-08-26 | E-MTAB-4953 | biostudies-arrayexpress

Yeast linker histone HHO1p effect on transcription before and after heat shock

Project description:DNA array expression analysis comparing RNA transcripts in wild type and hho1 strains before and after a heat-shock from 25 to 37 degrees. Keywords: expression, heat shock

2008-07-01 | GSE9095 | GEO

Yeast Sis1 proximity labelling during heat shock

Project description:Proximity interactome labelling of Sis1 APEX2 during heat shock revealed its comprehensive interactome.

2023-08-18 | PXD039068 | Pride

Dissecting the yeast heat shock response by CRISPRi/a

Project description:CRISPRi screens on the repression of 129 protein kinases and 161 transcription factors in S. cerevisiae. We quantify perturbation effects on cellular fitness at 23, 30 and 38°C, expression of the SSA1 Hsp70 chaperone (as proxy for heat shock response activity) and thermotolerance. The integration of these phenotypes allowed us to identify core signaling pathways of the HSR and their contributions to temperature-associated growth and heat resistance.

2021-07-01 | GSE155455 | GEO

The cold shock response of Bacillus subtilis analyzed by RNA-sequencing: YplP regulates pyruvate transport at low temperatures

Project description:The cold shock response of B. subtilis was defined after 0.5 hr and 2 hr cold shock using RNA sequencing. We identified novel RNAs (including non-coding RNAs) that play a role during growth at low temperatures. Deletion of the cold induced protein YplP results in a cold sensitive phenotype, and a comparative RNA sequencing analysis suggests that YplP induces pftAB expression after prolonged incubation at low temperatures, thereby optimizing pyruvate transport under cold shock conditions.

2018-03-12 | GSE111577 | GEO

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