Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

43 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Life cycle analysis of the model organism Rhodopirellula baltica by transcritpome studies

ABSTRACT: Gene expression was monitored throughout a growth curve of R. baltica culture: Cultures were harvested at different time points (44 h, 62 h, 82h, 96 h and 240 h) and compared with each other Two-condition experiment, one time point compared to another for each Sample.

ORGANISM(S): Rhodopirellula baltica

SUBMITTER: Patricia Wecker

PROVIDER: E-GEOD-19405 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Response of Rhodopirellula baltica to salt shift

Project description:Expression profiling of the stress response of the marine Planctomycete Rhodopirellula baltica after a salinity up-shift. R. baltica cultures were grown at 28Â°C in mineral media with 17.5% salinity and up-shifted to 59.9%. Samples were taken after 10, 20, 40, 60 and 300min and compared with cultures before the up-shift. Reference design, time series experiment Whole genome array 5 time points, 3 replicates per time point. In total, 18 samples.

2010-05-05 | E-GEOD-14075 | biostudies-arrayexpress

Response of Rhodopirellula baltica to heat shock

Project description:Expression profiling of the stress response of the marine Planctomycete Rhodopirellula baltica after a temperature up-shift. R. baltica cultures were grown at 28°C and then shifted to 37°C. Samples were taken after 10, 20, 40, 60 and 300min and compared with cultures before the up-shift (28°C). Time series experiment, whole genome array 5 time points, 3 replicates per time point. Each time point sample was compared with the reference. 3 self-self reference hybridizations. In total, 18 samples.

2009-09-09 | E-GEOD-13769 | biostudies-arrayexpress

Response of Rhodopirellula baltica to cold shock

Project description:Expression profiling of the stress response of the marine Planctomycete Rhodopirellula baltica after a temperature up-shift. R. baltica cultures were grown at 28Â°C and then shifted to 6Â°C. Samples were taken after 10, 20, 40, 60 and 300min and compared with cultures before the up-shift (28Â°C). Reference design, time series experiment Whole Genome Array 5 time points, 3 replicates per time point. 3 self-self reference hybridizations. In total, 18 samples.

2009-09-09 | E-GEOD-13856 | biostudies-arrayexpress

Nitrate Stress in Desulfovibrio vulgaris Hildenborough (Fur knockout : JW707)

Project description:Using data from microarray experiments, we investigated the effects of excess sodium nitrate on D. vulgaris. Keywords: stress response, time course Comparison of cells treated with 105 mM sodium nitrate to untreated cells at times of 0, 30, 60, 120, and 240 min.

2011-02-01 | E-GEOD-20092 | biostudies-arrayexpress

Nitrate Stress in Desulfovibrio vulgaris Hildenborough

Project description:Using data from microarray experiments, we investigated the effects of excess sodium nitrate on Desulfovibrio vulgaris. Keywords: stress response, time course Comparison of cells treated with 105 mM sodium nitrate to untreated cells at times of 0, 30, 60, 120, and 240 min.

2010-06-22 | E-GEOD-20079 | biostudies-arrayexpress

Combining transcriptomics with functional phylogenomics elucidates the ecophysiology of sulfatases in marine bacteria

Project description:We present a study combining gene expression analyses and bioinformatic assessment. 1120 sequences annotated as sulfatase encoding from eight Rhodopirellula strains were clustered into 173 groups of orthologous and paralogous genes. A selection of 709 sulfatase gene strains were aligned to 66 sulfatase genes of known function to check for their respective substrate specificity. Thereby, 22 major phylogenetic clusters were observed with just five being mixed clusters between Rhodopirellula and reference sequences. This indicates a huge diversity on the substrate recognition level, unexpected from conventional annotations in public databases. Exemplarily, Rhodopirellula baltica SH1T was grown on different sulfated polysaccharides. Subsequent gene expression analyses using whole genome microarrays revealed distinct sulfatase expression profiles based on substrates tested. Expression profiles strongly point towards a functional link between sulfated polysaccharides and sulfatases. Moreover, further potential functions can be deduced from the expression profiles. In silico assessment backed up in vivo findings and raised the question, whether related strains and species are even more adapted to utilizing sulfated polysaccharides present in marine environments. Dual channel microarrays have been used for comparing the gene expression of R. baltica SH1T under reference condition (grown on glucose) and grown on sulfated polysaccharides as substrates of interest. Substrates tested have been: Chondroitin sulfate, lambda carrageenan and fucoidan. Control: 3 Biological replicates, Substrates tested: 2-3 Biological replicates, 2-3 replicates per array

2012-03-31 | E-GEOD-35832 | biostudies-arrayexpress

Multiple mechanisms mediate the taurine-induced proliferation of neural stem/progenitor cells from the subventricular zone of the adult mouse

Project description:Taurine was previously reported to increase the proliferation of neural precursor cells (NPCs) from subventricular zone of the mouse brain. The results of a study that aimed to understand the mechanisms of this effect are presented here. A gene expression profile analysis indicated that genes regulated by taurine have roles in proliferation, cellular adhesion, cell survival, and mitochondrial functioning. Together with additional functional analyses, the results suggest that taurine provides more favorable conditions for cell proliferation by improving mitochondrial functioning. The total RNA from the control and taurine NPC cultures was used to produce tagged complementary DNA (cDNA) probes. Hybridation analysis used the mouse 65-mer oligo library from Sigma-Genosys to compare the expression of 23,232 gene-specific oligonucleotide probes for mouse.

2013-12-21 | E-GEOD-53547 | biostudies-arrayexpress

Transcriptome analysis of genes regulated by CUP-SHAPED COTYLEDON1 (CUC1) transcription factor in Arabidopsis thaliana

Project description:Samples 1 & 2: Comparison of gene expression between wild type (ecotype Ler) and 35S:CUC1, in which CUP-SHAPED COTYLEDON1, a master regulator of the shoot meristem and boundary establishment, is constitutively expressed under the cauliflower mosaic virus 35S promoter. Samples 3 & 4: Comparison of gene expression between stm-1 (ecotype Ler) and stm-1 35S:CUC1 RNA was isolated from cotyledons of 5-day-old (for Ler vs 35S:CUC1) or 10-day-old (for stm vs 35S:CUC1stm) seedlings. Two independent biological replicates were analyzed for each comparison.

2011-03-30 | E-GEOD-27482 | biostudies-arrayexpress

Transcriptome analysis of the Trypanosoma cruzi life-cycle

Project description:To generate a high quality, annotated gene expression database of T. cruzi trypomastigotes(TRP), amastigotes (AMA), epimastigotes (EPI), and metacyclic trypomastigotes (MET). The global assessment of transcript abundances in each life-cycle stage of T. cruzi will identify stage-regulated genes and provide an essential element of an integrated database of T. cruzi genomic, proteomic, and transcriptomic data. RNAs from 3 biological replicates from a single time point in each stage will be subjected to DNA microarrays containing probes for the complete, annotated T. cruzi genome, as it is currently known. The arrays for this project will be provided by the Pathogen Functional Genomics Resource Center (PFGRC) at The Institute for Genomic Research (TIGR) sponsored by the National Institute of Allergy and Infectious Diseases (NIAID), and will contain long oligonucleotides complementary to every annotated gene in the newly sequenced T. cruzi genome. The resulting data and analysis results will be deposited in TcruziDB (http://TcruziDB.org). Keywords: Gene expression comparisons between the four life-cycle stages of T. cruzi Six hybridizations were performed for each life-cycle stage. The hybridizations consisted of three dye-swap experiments from three independent samples (biological replicates). In each case, the experimental sample was from a single life-cycle stage and the control sample was an equal mixture of all four life-cycle stages. A total of 24 hybridizations were preformed.

2010-05-15 | E-GEOD-14641 | biostudies-arrayexpress

Proteomic analysis of psychrophilic and mesophilic bacterial species

Project description:This study, in an attempt to mimic the molecular adaptation of polar microorganisms, combines proteomic approaches with a classical microbiological analysis in several bacterial species. The comparison of the strategies employed by each bacterial species estimates the contribution of genome versus environmental variables in the adaptation to temperature. Regarding the molecular machinery used by these bacteria to face the consequences of temperature changes, chaperones have a pivoting role. They form complexes with other proteins in the response to the environment, establishing cooperation with transmembrane proteins, elongation factors, and proteins for protection against oxidative damage.

2021-12-16 | PXD030438 | Pride

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