Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq based transcriptome of Nesterenkonia sp. AN1

ABSTRACT: The transcript profiles of Nesterenkonia sp. AN1 grown at 5 ºC (Cold) and 21 ºC (Topt) were acccessed to evaluate the cold reposnse of this Antarctic Nesterenkonia strain. The strain was grown in triplicates at the optimum growth temperature of 21 ºC and a test temperature of 5 ºC. Total RNA was extracted from two replicate samples for each treatment condition and the total RNA was enriched for mRNA. RNA-seq was done using Illumina Miseq platform at Inqaba Biotech, South Africa. The reads were mapped against the genome sequence of Nesterenkonia sp. AN1 (obtained from NCBI database) and assesed for differeential gene expression using CLC Genomics Workbench 7.5.

ORGANISM(S): Nesterenkonia sp. AN1

PROVIDER: GSE71132 | GEO | 2015/07/22

SECONDARY ACCESSION(S): PRJNA290435

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq based transcriptome of Nesterenkonia sp. AN1

Project description:The transcript profiles of Nesterenkonia sp. AN1 grown at 5 ºC (Cold) and 21 ºC (Topt) were acccessed to evaluate the cold reposnse of this Antarctic Nesterenkonia strain. The strain was grown in triplicates at the optimum growth temperature of 21 ºC and a test temperature of 5 ºC. Total RNA was extracted from two replicate samples for each treatment condition and the total RNA was enriched for mRNA. RNA-seq was done using Illumina Miseq platform at Inqaba Biotech, South Africa. The reads were mapped against the genome sequence of Nesterenkonia sp. AN1 (obtained from NCBI database) and assesed for differeential gene expression using CLC Genomics Workbench 7.5. Evaluation of RNA-seq data for Nesterenkonia sp. AN1 at 5 ºC (Cold) and 21 ºC (Topt) in two biological replicates

2015-07-22 | E-GEOD-71132 | biostudies-arrayexpress

Proteomic study at low and optimum temperature in Pseudomonas sp. Lz4W using LC-MSMS

Project description:Proteomic analysis of an Antarctic bacterium Pseudomonas sp. Lz4W by tandem mass spectrometry to unveil the process of cold adaptation. Comparative whole proteome analysis was performed at Low and optimum temperature.

2022-03-17 | PXD029741 | Pride

Proteomics of psychrotolerant Trichococcus patagoniensis and characterization of the produced exopolysaccharides as inulin

Project description:The psychrotolerant Trichococcus patagoniensis was previously reported to produce exopolysaccharides (EPS) that covers the cells, when grown at a low temperature. Although, T. patagoniensis has an optimal growth at 30 ºC, it still can grow at -5 ºC. This capability of T. patagoniensis to grow at subzero temperatures is expected to be reflected in the proteome, membrane lipid composition and/or EPS production. This study aimed to get insight into the cold adaptation mechanisms of T. patagoniensis. We compared the proteomes of cells grown at 0 and 30 ºC and the EPS that is formed.

2022-08-12 | PXD011268 | Pride

Differential proteomic analysis by SWATH-MS unravels the most dominant mechanisms underlying yeast adaptation to nonoptimal temperatures under anaerobic conditions- SWATH data

Project description:Elucidation of the mechanism of temperature tolerance in yeast is essential for enhancing cellular robustness of strains, providing more economically and sustainable sound industrial processes. We investigated the differential responses of three distinct Saccharomyces cerevisiae strains, an industrial wine strain, ADY5, a laboratory strain, CEN.PK113-7D and an industrial bioethanol strain, Ethanol Red, grown at sub- (12 ºC) and-supra (39 ºC) optimal temperatures under chemostat conditions, in which specific growth rate–dependent changes are eliminated. In contrast to previous studies, we employed anaerobic conditions, mimicking the industrial processes. The proteomic profile of these strains was performed by SWATH-MS, allowing the quantification of 997 proteins. Our analysis revealed that temperature response differs between the strains, highlighting the precision with which each strain responds to changes in its environment; however, we also found some common responsive proteins among the strains, revealing that the response to temperature involves general stress and specific mechanisms. Overall, sub-optimal temperature conditions involved a higher remodeling of the proteome than supra-optimal temperature. Further, the proteomic data evidenced that the cold response involves a strong repression of translation related proteins as well as induction of amino acid metabolism, together with components related to protein folding and degradation. On the other hand, the high temperature response mainly recruits amino acid metabolism. Our study provides a global and thorough insight into how growth temperature affects yeast proteome, which can be a step forward for research regarding the comprehension and the improvement of yeast thermotolerance.

2021-01-04 | PXD016567 | Pride

Arabidopsis thaliana roots: inoculated roots with a bacterium Antarctic (Pseudomonas sp, Dac-bac TI-8) vs untreated roots (control)

Project description:Transcriptional profiling of Arabidopsis thaliana roots comparing inoculated roots with a bacterial strain Antarctic (Pseudomonas sp, Da-bac TI-8) vs untreated roots (control)

2013-03-28 | GSE45559 | GEO

Global phenotypic and genomic comparison of two Saccharomyces cerevisiae wine strains

Project description:The aim of this study is to phenotype a collection of 27 S. cerevisiae commercial wine strains growing within temperatures (4-45ºC) in both minimal media (SD) and synthetic must (SM) and, taking into account µmax value, to select two strains with divergent phenotype in their capacity to grow at low temperature. To confirm this differential phenotype, we design a competition between both strains during wine fermentations. As expected, at low temperature fermentation, the strain showing a good performance out-competes to the strain growing badly in cold. Finally we aimed to decipher the molecular basis underlying this divergent phenotype by analyzing the genomic, proteomic and transcriptomic differences between both strains at low temperature (15ºC) and optimum temperature (28ºC).

2015-03-31 | GSE60140 | GEO

Shene2020 - flux balance analysis of biomass and lipid production by Antarctic thraustochytrid Oblongichytrium

Project description:Modelo_mod3_032020.m is a Matlab code used for the simulation of the growth curve of Antarctic thraustochytrid Oblongichytrium sp. RT2316-13. The model is based on the genome scale model adapted for the strain that is found in the Excel file ExcelAurant_28102019.xlsx. Flux balance analysis is used to predict the specific growth rate of the biomass, specific synthesis of neutral lipids and specific consumption rate of the nutrients. The code crea_modelo.m transform the excel file into the array model_T.mat used in by Modelo_mod3_032020.m This model was used to generate data presented in the manuscript Dynamic flux balance analysis of biomass and lipid production by Antarctic thraustochytrid Oblongichytrium sp. RT2316-13, 2020, Carolina Shene, Paris Paredes, Liset Flores, Allison Leyton, Juan A. Asenjo, Yusuf Chisti, Biotechnology and Bioengineering, DOI: 10.1002/bit.27463.

2020-07-16 | MODEL2006010001 | BioModels

Expression Profile of R. capsulatus under heat and cold stress

Project description:The effects of temperature stress on transcriptome of purple non sulfur bacterium R. capsulatus were investigated by comparing expression profiles under optimum hydrogen production condition (30°C), heat (42°C) and cold (4°C) stress conditions.

2013-12-19 | GSE53477 | GEO

Microarray transcriptional profiling of Arctic Mesorhizobium strain N33 at low temperature provides insights into cold adaption strategies

Project description:Arctic Mesorhizobium strain N33 was isolated from nodules of the Oxytropis arctobia in Canada’s eastern Arctic. This symbiotic bacterium can grow from 0 to 30°C, is one of the best known cold-adapted rhizobia, and can fix nitrogen at ~10°C. Here, the key molecular mechanisms of cold adaptation were investigated by determining changes in transcript profiles when cells were treated under eight different temperature conditions, including both sustained and transient cold treatments compared with cells grown at room temperature.

2015-05-08 | GSE60710 | GEO

Functional genomic analysis of cold acclimation in the genus Solanum

Project description:Healthy five-weeks old S. tuberosum (Red Pontiac) and S. commersonii (Oka 5040) were subjected to cold-acclimating temperature (2oC) in the growth chamber. Control plants at identical developmental stage were also grown in growth chamber at optimum conditions for growth (28oC, 14/10, light/dark, 65% RH). Leaf tissues were collected from the control (reference) and cold-acclimating (experimental treatment, 2oC) plants for each species at 2, 4, 7, 10 and 14 days after the initiation of the control and low temperature treatments. A total of two plants for each species were used for both the control and treatment experiments and tissue samples from each plant (within replicate) were pooled for RNA isolation. These experiments were performed twice in order to produce two sets of biological replicates for each species for all sampling time-points. Keywords: Reference design

2007-09-01 | GSE8281 | 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