Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ribo-seq analysis of Saccharomyces cerevisiae with and without 10 minute glucose starvation

ABSTRACT: Ribosome profiling (Ribo-Seq) and RNA-Seq analysis of Saccharomyces cerevisiae with and without 10 minute glucose starvation to determine effects on translation.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Michael Nelson

PROVIDER: E-MTAB-9094 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq

Project description:We present a genome-wide assessment of small open reading frames (smORF) translation by ribosomal profiling of polysomal fractions in Drosophila S2 cell. In this way, mRNAs bound by multiple ribosomes and hence actively translated can be isolated and distinguished from mRNAs bound by sporadic, putatively non-productive single ribosomes or ribosomal subunits. Ribosomal profiling of large and small polysomal fractions in Drosophila S2 cells to assess translation of smORFs

2014-09-11 | E-GEOD-60384 | biostudies-arrayexpress

Analysis of P-body (Dcp1) and Stress Granule (Pbp1) RNA content

Project description:Non-membrane-bound compartments such as mRNA processing bodies (PBs) and stress granules (SGs) play important roles in the regulation of gene expression following environmental stresses. Here we perform RIP-seq to determine the RNA interactors of Dcp1 (PB marker) and Pbp1 (SG marker) before and after an appropriate glucose stress.

2021-09-30 | E-MTAB-9096 | biostudies-arrayexpress

Evolution at two regulatory levels in yeast

Project description:Ribosome profiling performed on interspecific hybrids of Sacharromyces cerevisiae and S. paradoxus in order to identify allele-specific expression indicative of cis-regulatory divergence at the level of mRNA abundance and protein translation. Two biological replicate libraries sequenced from ribosome protected fragments as well as poly-A-selected mRNA of hybrids in addition to one biological replicate library of poly-A selected mRNA from each parental strain.

2013-11-29 | E-GEOD-50049 | biostudies-arrayexpress

Genome-Wide Translation Profiling by Ribosome-Bound tRNA Capture

Project description:In the ribosome complex, tRNA is a critical element of mRNA translation. We reported a new technology for profiling ribosome-embedded tRNAs and their modifications. With the method, we generated a comprehensive survey of the quanity and quality of intra-ribosomal tRNAs (Ribo-tRNA-seq). Ribo-tRNA-seq can provide new insights on translation control mechanism in diverse biological contexts.

2018-03-19 | E-MTAB-6576 | biostudies-arrayexpress

Ribo-Seq transcriptomic analysis of human RD cells infected with enterovirus strains EV7, EV71, and PV1.

Project description:Ribosome profiling (Ribo-Seq) (maps positions of translating ribosomes on the transcriptome) analysis of human (RD) cells infected with enterovirus strains EV7, EV71, and PV1.

2018-10-19 | E-MTAB-6180 | biostudies-arrayexpress

Differential protein expression in new1 knock-out yeast

Project description:A label-free quantitative proteomics experiment was performed to study the impact of new1 knock-out on differential protein expression in S. cerevisiae (baker’s yeast).

2024-11-26 | PXD055983 | Pride

Ribosome profiling of NEW1 knock-out as well as the isogenic wild type strain of Saccharomyces cerevisiae. The cultures were grown either at 20°C or 30°C.

Project description:Loss of New1 leads to a cold-sensitive phenotype of yeast Saccharomyces cerevisiae. In this study we investigated the effect of NEW1 knockout on translation using Ribo-Seq and RNA-Seq analyses.

2019-05-31 | E-MTAB-7763 | biostudies-arrayexpress

Ribosome profiling of NEW1 knock-out of budding yeast Saccharomyces cerevisiae

Project description:New1 is not an essential gene but its deletion shows a cold-sensitive phenotype in yeast Saccharomyces cerevisiae. In this study, we compare the NEW1 knockout effect on translation using Ribo-Seq and RNA-Seq analyses.

2018-11-10 | E-MTAB-6963 | biostudies-arrayexpress

Ribosome profiling upon glucose starvation in S. cerevisiae

Project description:A universal feature of the response to stress and nutrient limitation is transcriptional upregulation of genes encoding proteins important for survival. Interestingly, under many of these conditions overall protein synthesis levels are reduced, thereby dampening the stress response at the level of protein expression. For example, during glucose starvation in yeast, translation is rapidly and reversibly repressed, yet transcription of many stress- and glucose-repressed genes is increased. Using ribosome profiling and microscopy, we found that this transcriptionally upregulated gene set consists of two classes: (1) one producing mRNAs that are preferentially translated during glucose limitation and are diffusely localized in the cytoplasm – this class includes many heat shock protein mRNAs; and (2) another producing mRNAs that are poorly translated during glucose limitation, have high rates of translation initiation, and are concentrated in foci that co-localize with P bodies and stress granules – this class is enriched for glucose metabolism mRNAs. Remarkably, the information specifying differential localization and translation of these two classes of mRNAs is encoded in the promoter sequence – promoter responsiveness to heat shock factor (Hsf1) specifies diffuse cytoplasmic localization and preferential translation upon glucose starvation, whereas different promoter elements upstream of genes encoding poorly translated glucose metabolism mRNAs direct these mRNAs to RNA granules under glucose starvation. Thus, promoter sequences and transcription factor binding can influence not only mRNA levels, but also subcellular localization of mRNAs and the efficiency with which they are translated, enabling cells to tailor protein production to environmental conditions. Examination of mRNA translation in S. cerevisiae upon glucose starvation.

2014-07-28 | E-GEOD-56622 | biostudies-arrayexpress

Analysis of RIP-seq of Ded1 and eIF4A(Tif1) with and without glucose depletion

Project description:The aim of this experiment was to look at RNAs which associate with DEAD-box RNA helicases with and without 10 minutes of glucose starvation.

2021-09-30 | E-MTAB-9095 | 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