Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

42 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Translation profiling of Schizosaccharomyces pombe size separated polysome fractions provides data on average numbers of associated ribosomes for most transcripts

ABSTRACT: To obtain translational profiles for all mRNAs, polysome preparations are separated according to their size using a sucrose gradient and the mRNAs in each fraction are identified and quantified with DNA microarrays. Starting with exponentially growing cells, we analyzed 12 polysome fractions using DNA microarrays containing elements for all known and predicted genes of fission yeast. This approach provided data on average numbers of associated ribosomes for most transcripts.

INSTRUMENT(S): Axon GenePix 4000B scanning hardware

ORGANISM(S): Schizosaccharomyces pombe

SUBMITTER: Daniel Lackner

PROVIDER: E-TABM-222 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

A network of multiple regulatory layers shapes gene expression in fission yeast.

Lackner Daniel H DH Beilharz Traude H TH Marguerat Samuel S Mata Juan J Watt Stephen S Schubert Falk F Preiss Thomas T Bähler Jürg J

Molecular cell 20070401 1

Gene expression is controlled at multiple layers, and cells may integrate different regulatory steps for coherent production of proper protein levels. We applied various microarray-based approaches to determine key gene-expression intermediates in exponentially growing fission yeast, providing genome-wide data for translational profiles, mRNA steady-state levels, polyadenylation profiles, start-codon sequence context, mRNA half-lives, and RNA polymerase II occupancy. We uncovered widespread and ...[more]

PMID: 17434133

Similar Datasets

Poly(A) tail length profiling of mRNAs from fission yeast

Project description:To obtain global data on polyadenylation of mRNAs, we fractionated the mRNAs according to their poly(A) tail length using a poly-U sepharose column followed by differential elution at five temperatures. Five mRNA fractions with distinct ranges of poly(A) tail length were then hybridized to microarrays using total eluate as a reference.

2007-05-16 | E-TABM-217 | biostudies-arrayexpress

Transcription profiling of Arabidopsis infected with Tobacco etch virus (TEV), a potyvirus vs healthy plants

Project description:In this experiment, Arabidopsis plants infected by a virus, Tobacco etch virus (TEV), a potyvirus, were compared with healthy plants to identify genes for which the expression is modified by the viral infection. Analysis of both inoculated leaves and upper young leaves were performed 7 days after the inoculation with the virus (or with only buffer for the healthy plants).

2005-11-01 | E-MEXP-364 | biostudies-arrayexpress

Transcription profiling of Arabidopsis wild type, AtVdac1 knock-outs, p26 knock-outs and AtVdac1-p26 double kock-outs in response to growth in medium with salicylic acid

Project description:Functions of AtVDAC1 and its partner p26 in Arabidopsis thaliana. We previously showed that knock-out mutants impaired in AtVdac1 and p26 (AtVdac1 protein partner) are hypersensitive to salicylic acid: the root growth is more inhibited in response to 30 uM salicylic acid (SA) compared to the wild type. We want to know now which genes are up- or down-regulated in the mutants in control and SA conditions. We want to compare the RNAm contents in the wild type, vdac1 and p26 mutants and, vdac1-p26 double mutant. One-week old plantlets were transferred for 2 hours on a fresh medium containing either 0 or 30uM salicylic acid. Arabidopsis lines (WT, vdac1.1, p26.1, vdac1.1-p26.1) were grown in vertical position on ABIS medium (Lanquar et al., 2006). One week-old seedlings were transferred on a fresh ABIS medium containing either 0 or 30 uM salicylic acid. After 2 hours, the all seedlings were harvested. Three replicates were done; total RNAs from these 3 experiments were mixed together for the transcriptomic analysis.

2007-06-19 | E-MEXP-795 | biostudies-arrayexpress

Transcription profiling of wild type and atNRT2.7 genotype Arabidopsis leaves and roots grown in high or low nitrate conditions

Project description:Does the NRT2.7 participate to the HATS? We would like to understand the function of the AtNRT2.7 in nitrate transport under limiting and non limiting nitrate conditions. Plants were harvested after 32 days for plants under high nitrogen nutrition and 42 days for low nitrogen nutrition. Plants were grown hydroponic condition (short day, 170 uE).

2007-07-01 | E-MEXP-801 | biostudies-arrayexpress

Transcription profiling of Arabidopsis thioredoxin reductase knock-out mutant

Project description:Transcriptomic study of a thioredoxin reductase knock-out mutant. Biological question : Thioredoxins are small redox proteins implicated in crucial pathways of cell life. They are reduced by a conserved flavoprotein named NADPH-dependent thioredoxin reductase (NTR). In order to give an insight into the functions of the NTR/thioredoxin pathway in Arabidopsis, we have used a reverse genetic approch. Both NTR genes (NTRA and NTRB) have been inactivated in the double ntra ntrb mutant. T-DNA lines have been provided by the SALK library. Surprisingly, this mutant shows a limited phenotype suggested that some additional redox pathways are involved in compensating the inactivation of the NTR/thioredoxin pathway. In order to isolate compensatory genes that would be transcriptionally induced in the ntra ntrb mutant, we have performed this CATMA project. Seeds of the wild-type Col-0 ecotype and of the ntra ntrb homozygote double mutant were sowed in soil. Three replicates of lines were made (Col-0 1, 2 and 3 ntra ntrb 1, 2 and 3) : plants were put at different places of the greenhouse and grown at different times. Germination was synchronized by 4 days at 4C and plants were grown during 17 days, until they reached a 6 rosette leaves stage. Entire plants (30 plants per sample) were harvested, frozen in liquid nitrogen and stored at -80C until extraction.

2005-09-15 | E-MEXP-365 | biostudies-arrayexpress

Transcription profiling of Arabidopsis treated with seaweed extract vs those grown hydroponically

Project description:Columbia Arabidopsis ecotype were grown hydroponically on 1 mM NH4NO3 as sole nitrogen source during 35 days under short days. Plants leaves were then sprayed with a seaweed extract or with water (control). Root and shoot samples were harvested separately 1 hour and 7 days after this spraying.

2007-01-26 | E-MEXP-573 | biostudies-arrayexpress

Transcription profiling of cold and phosphlipase treated Arabidopsis tto analyse the effect of Phospholipases C and D

Project description:The study aims at determining the genes that are induced or repressed by cold in the suspension cells. It also aims at monitoring the effect of inhibitors of PLC (U73122 vs. U73343) and PLD (ethanol vs. tertiary butanol) on cold response at the transcription level. To answer this question we chose a pharmacological approach. We decided to use molecules that are going to inhibit PLC or PLD. For PLC we use U73122 and its inactive analog as a control; for PLD we used a primary alcohol (ethanol) and a tertiary alcohol (tert-butanol) as a control. We therefore extracted RNA after the following treatments: 4 °C 22 °C 4 °C + 0.9% primary-ethanol 4 °C + 0.9% tertiary-butanol 4 °C + 60 micromolaire U73122 4 °C + 60 micromolaire U73343 The exposure at 4 °C was 4 hours.

2005-08-26 | E-MEXP-259 | biostudies-arrayexpress

Transcription profiling of Arabidopsis nin7-1 and nin7-2 in a low nitrogen regime

Project description:Does the ko of NIN7 leads to a differential expression in comparison to the wildtype. Can we repeat the results from the first experiment; and is there a difference between the two alleles? Plants were harvested during the first 3 hours of light after 42 days growth on 0.2mM or 6mM nitrate in hydroponic condition (short day, 170 uE).

2006-12-19 | E-MEXP-516 | biostudies-arrayexpress

Transcription profiling of Arabidopsis in standards condition and in response to nickel treatment to assess the effect nicotianamine over-accumulation on the transcriptome of A. thaliana

Project description:Effect of nicotianamine over-accumulation on the transcriptome of A. thaliana in standard condition and in response to nickel treatment After germination, plants were grown hydroponically for 6 weeks in classical nutrient solution (Marques et al, New Phytol, 2004, vol 164, pp 289-95) and then treated for 48 hours with 50 uM NiSO4 or with no nickel added for control. Biological question : Nicotianamine is a known metal chelator (of Mn, Fe, Zn, Ni, Cu) suspected to be involved in metal delivery and/or circulation in planta. This project aim at understanding the effect of the modulation of the nicotianamine content on the transcriptome of Arabidopsis thaliana in control hydroponic condition and in response to nickel treatment both at the root and at the leaf level.

2006-06-01 | E-MEXP-373 | biostudies-arrayexpress

Transcription profiling of Arabidopsis after 12 or 24 hours growth in fresh medium with or without cadmium

Project description:After 5 days of grown in a fresh medium (5% PCV at day0), CdCl2 was added to tested cells (Cad) to a final concentration of 200uM. Nothing was added to control cells (Tem). After 12 and 24 hours of growth +/- cadmium, cells were harvested and frozen in liquid nitrogen.

2007-07-20 | E-MEXP-797 | 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