Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Rhizobium etli CFN42 wild type transcriptional profiling was compared between free living and symbiosis conditions

ABSTRACT: Rhizobium etli is a bacteria that fix nitrogen in symbiotic activity with Phaseolus vulgaris, the common bean plant. In order to accomplish this nitrogen reduction a especial environment is induced in nodules such that gene expression of bacteroid suffer a significant change with respect to its wild type life style. With the purpose to identify genetic alterations between these physiological states, replicates of microarray data were accomplished in similar conditions between bacteria cultivated in free-life (succinate-ammonia) and those carrying on nitrogen fixation inside nodule. Three independent biological materials with one dyeswap were performed.

ORGANISM(S): Rhizobium etli CFN 42

SUBMITTER: Sergio Encarnación

PROVIDER: E-GEOD-21638 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Systems biology of bacterial nitrogen fixation: high-throughput technology and its integrative description with constraint-based modeling.

Resendis-Antonio Osbaldo O Hernández Magdalena M Salazar Emmanuel E Contreras Sandra S Batallar Gabriel Martínez GM Mora Yolanda Y Encarnación Sergio S

BMC systems biology 20110729

<h4>Background</h4>Bacterial nitrogen fixation is the biological process by which atmospheric nitrogen is uptaken by bacteroids located in plant root nodules and converted into ammonium through the enzymatic activity of nitrogenase. In practice, this biological process serves as a natural form of fertilization and its optimization has significant implications in sustainable agricultural programs. Currently, the advent of high-throughput technology supplies with valuable data that contribute to u ...[more]

PMID: 21801415

Similar Datasets

Murine livers post DEN treatment: c-Jun f/f vs. c-Jun Dli

Project description:This SuperSeries is composed of the following subset Series: GSE39928: Murine livers post DEN treatment: c-Jun f/f vs. c-Jun Dli [35MM] GSE39929: Murine livers post DEN treatment: c-Jun f/f vs. c-Jun Dli [40MM] GSE39930: Murine livers post DEN treatment: c-Jun f/f vs. c-Jun Dli [41MM] GSE39931: Murine livers post DEN treatment: c-Jun f/f vs. c-Jun Dli [43MM] Refer to individual Series ** Six samples in each Series represent the same set of biological source material hybridized to 4 different arrays (named IMP internal: 35MM, 40MM, 41MM, and 43MM).

2012-08-07 | E-GEOD-39932 | biostudies-arrayexpress

Murine livers post DEN treatment: c-Jun f/f vs. c-Jun Dli [41MM]

Project description:Liver carcinogenesis induced by DEN closely mimics the pathologies observed during human liver tumor initiation and progression. DEN treatment triggered c-Jun expression lasting up to at least 1 week in mouse livers as measured by Western blots and immunohistochemical staining. DEN-induced liver tumorigenesis was also dramatically reduced in Alfp-cre+/c-jun f/f mice, in which c-Jun is constitutively deleted in hepatocytes around birth. These data unambiguously demonstrate that c-Jun is specifically required during liver cancer initiation. We searched for cell death effectors downstream of c-Jun operating in cancer initiation. Expression profiling revealed that several cell death-associated genes were deregulated by comparing Alfp-cre+/c-junf/f and Alfp-cre-/c-jun f/f livers. Mouse livers were collected before and 48hours after diethylnitrosamine treament (100mg/kg body weight). Whole genome expression profiles were analyzed using total RNAs extracted from the whole liver samples. By comparison of the gene expression profiles of these samples, genes with significantly altered expression levels will be selected and further characterized for their roles in DEN-induce liver cell death in tumor initiation.

2012-08-07 | E-GEOD-39930 | biostudies-arrayexpress

Murine livers post DEN treatment: c-Jun f/f vs. c-Jun Dli [40MM]

2012-08-07 | E-GEOD-39929 | biostudies-arrayexpress

Murine livers post DEN treatment: c-Jun f/f vs. c-Jun Dli [43MM]

2012-08-07 | E-GEOD-39931 | biostudies-arrayexpress

Murine livers post DEN treatment: c-Jun f/f vs. c-Jun Dli [35MM]

2012-08-07 | E-GEOD-39928 | biostudies-arrayexpress

ClpP protease modulates bacterial growth, stress response and bacterial virulence in Brucella abortus

Project description:Intracellular proteolysis via ATP-dependent proteases is a conserved biological process. The ATP-dependent Clp protease is made up of peptidase ClpP and ATP-dependent chaperones and plays an important role in the proteolysis process. In several pathogenic bacteria, the Clp protease is implicated in the stress reponses and contributes to the bacterial virulence. In brucella abortus, the ΔclpP mutant strain exhibited a pronounced growth defect in TSB medium and the results showed that the ΔclpP mutant was sensitive to high temperature, high osmotic environment and iron deficient environment. In addition, deletion of the clpP significantly affected Brucella virulence in macrophage and mice infection models. Based on the iTRAQ analysis, the different expressed proteins were mainly involved in amino acid transport and metabolism, energy production and conversion, and secondary metabolites biosynthesis, transport and catabolism. Overall, our study revealed preliminary molecular mechanism between Clp protease, bacterial growth, stress response and bacterial virulence in Brucella strains

2023-10-24 | PXD034842 | Pride

Gene Expression in Perivenous Hepatocytes: A Laser Capture Microdissection and Transcriptomic Analysis.

Project description:Differential expression of genes and proteins, as well as physiological processes, along the hepatic acinus, known collectively as hepatic zonation, is a fundamental feature of hepatic physiology. However, the precise cellular location of only a relatively small proportion of the ~14,000 genes expressed in the liver is known. This is critical information for understanding hepatic physiology as well as for the accurate targeting of gene transfer vectors for gene therapy. We have employed laser capture microdissection (LCM) and unbiased transcriptomic analysis of the normal adult mouse liver to define gene expression in a very distinct population of cells in the acinus, the glutamine-synthetase sub-compartment of perivenous hepatocytes, encompassing a one- to two-layer of cells surrounding the centrilobular vein. We confirmed the location of a number of genes whose expression is known to be restricted to these cells by virtue of immunohistochemistry or in situ hybridization (Slc1a2, Glul, Rhbg). We also identified genes whose expression had not previously been reported to be enriched in these cells (e.g. Sp5, Vldlr, Lpl, Gabrb3, Rcan2). Transcription factor analysis of the differentially expressed genes suggested important roles, in these cells, for members of the polycomb group, Wt1 and Tbx3. Collectively, our findings highlight the utility of combined LCM and transcriptome analysis for the identification of novel functions of distinct subclasses of hepatocytes. We plan to extend this approach to the mapping of physiological function across hepatic acini of the human liver. Comparison of mRNA expression by two hepatic cell populations: the glutamine synthetase-subcompartment of the perivenous compartment and zones 1+2 of the hepatic acinus Cells were isolated by laser capture microdissection and mRNA extracted by standard protocol.

2013-06-26 | E-GEOD-48273 | biostudies-arrayexpress

Optimal Processing for Proteomic Genotyping of Single Human Hairs

Project description:The human hair proteome offers new insight in the field of human identification. Hair often contains DNA that has been degraded due to the process of cornification. The smaller fragments of DNA present a challenge for obtaining useful information concerning the identity of the donor. Proteomic genotyping offers an alternative approach which starts with protein, a biomolecule abundant in the hair shaft. Nonsynonymous single nucleotide polymorphisms may be detected in the sequence of these proteins, allowing the inference of SNP genotypes. Population genetics-based information from these genotypes may be used to calculate random match probability or even infer ancestry. The current challenge of this research is to optimize processing chemistry in order to maximize genetic information from a single human hair shaft. Results indicate that optimal conditions for proteomic analysis of a single human hair include 6 hrs of reduction with 100 mM dithiothreitol at room temperature, alkylation with 200 mM iodoacetamide for 45 min, and 6 hrs of digestion with two 1:50 (enzyme:protein) additions of stabilized trypsin at room temperature, with stirring incorporated into all three steps. Our final conditions using optimized temperatures and incubation times for disulfide reduction and protein digestion produced random match probabilities of up to 1 in 624 million from a single hair with a median value of 1 in 1.1 million, compared to a maximum random match probability of 1 in 1380 and a median value of 1 in 24 for the original processing method.

2020-06-10 | PXD016155 | Pride

Characterisation of two in vivo expressed methyltransferases of the Mycobacterium tuberculosis complex: antigenicity and genetic regulation

Project description:Genome sequencing of Mycobacterium tuberculosis complex members has accelerated the search for new disease control tools. Antigen mining is one area that has benefited enormously from access to genome data. Here genes that were identified by transcriptome analysis as upregulated in response to an in vitro acid shock were screened for their in vivo expression profile and antigenicity. We show that the genes encoding two methyltransferases of Mycobacterium bovis, Mb1438c and Mb1440c, were highly upregulated in a mouse model of infection, and were antigenic in cattle infected with M.bovis. To define the regulation of the genes encoding these antigens we constructed a mutant that was deleted for their putative regulator, and showed that loss of the regulator led to increased expression of the flanking methyltransferases. This work has therefore generated both applied and fundamental outputs, with the description of novel mycobacterial antigens that can now be moved into field trials, but also with the description of a regulatory network that is responsive to both in vivo and in vitro stimuli. Data is also available from <ahref=http://bugs.sgul.ac.uk/E-BUGS-59 target=_blank>BuG@Sbase</a>

2008-01-09 | E-BUGS-59 | biostudies-arrayexpress

Bisulfite sequencing of wild type Arabidopsis plants and H1 mutants

Project description:Experiment was performed to assess the effect of H1 histones knock-out on DNA methylation under control conditions and a role of H1.3 in maintaining stress-induced menthylation response.

2015-01-21 | E-MTAB-2807 | biostudies-arrayexpress

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