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Oncogene_effect-Transcriptome alterations by the 6b oncogene of Agrobacterium

ABSTRACT: rs03-01_onc6b - oncogene_effect - The oncogene 6b affects the plant growth at the leaf, root, stem and flower level. The protein is localized in the nucleus and is suspected to modify transcription. - Effects of the activation of the oncogene 6b on the transcriptome Keywords: gene knock in (transgenic)

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE7993 | GEO | 2007/06/20

SECONDARY ACCESSION(S): PRJNA100773

REPOSITORIES: GEO

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dex-gvg-Transcriptome alterations by the 6b oncogene of Agrobacterium

Project description:rs03-01_onc6b - dex-gvg - The oncogene 6b affects the plant growth at the leaf, root, stem and flower level. The protein is localized in the nucleus and is suspected to modify transcription. - Observation of the effect of Dex-GFP expression on the transcriptome (control) Keywords: gene knock in (transgenic)

2007-06-20 | GSE8062 | GEO

Induction of tobacco genes by Agrobacterium oncogene 6b

Project description:Tumor induction by Agrobacterium is due to transfer of T-DNA genes. We study the 6b T-DNA oncogene that induces tumors on species like Nicotiana glauca, but for which no precise growth induction mechanism has been found sofar. The 6b gene belongs to a larger group of T-DNA genes including rolB, rolC and orf13, no homologies are known with other genes. In N. tabacum, 6b modifies responses to auxins and cytokinins and induces strong morphological changes including cell enlargement, abnormal division, double flowers, enations and root shortening (Helfer et al., 2003, Grémillon et al., 2004). Others have localized 6b and rolB proteins in the nucleus, where they could modify transcription (Kitakura et al., 2002, Moriuchi et al., 2004). Recently, we developed a system to study early 6b-induced growth changes, using a dexamethasone-inducible 6b gene (dex-T-6b). Leaves of homozygous dex-T-6b plants are infiltrated with a 10 mM MgSO4 solution, with or without 20 micromolar dex. In the presence of dex, a reproducible increase in glucose and fructose concentrations is observed. Such changes are also found in cultured leaf discs and in that case accompanied by an increase in expansion. 6b-induced changes are detected as early as 7 hours after dex infiltration. Western analysis shows that dex-T-6b plants have undetectable 6b protein levels without induction, and rapidly accumulate 6b protein upon induction. We propose to study gene expression in induced and non-induced leaves at different times of induction: 0-3-6-9 and 12 hours. The data will be used to establish whether the 6b gene induces specific genes, and whether these genes are involved in hexose changes and cell expansion. We will also test the effect of infiltrating tobacco leaves with 10 mM MgSO4 by comparison with non-infiltrated leaf tissues in order to correct for changes due to the infiltration procedure. Keywords: Reference design

2007-09-01 | GSE8235 | GEO

Human herpesvirus 6B (HHV-6B) detection and genome-wide host expression profiles implicate HHV-6B as a pulmonary pathogen after hematopoietic cell transplantation

Project description:Limited understanding of the immunopathogenesis of human herpesvirus 6B (HHV-6B) has prevented its acceptance as a pulmonary pathogen after hematopoietic cell transplantation (HCT). We conducted a prospective multicenter study of patients undergoing bronchoalveolar lavage (BAL) for pneumonia after allogeneic HCT. We tested blood and BAL fluid (BALF) for HHV-6B DNA and mRNA transcripts associated with lytic infection and performed RNA-seq on paired blood. Among 116 participants, HHV-6B DNA was detected in 37% of BALs, 49% of which had HHV-6B mRNA detection. We established an HHV-6B DNA threshold (≥2.3 log10copies/ml in BALF) that was highly predictive of HHV-6B mRNA detection and increased risk for death from respiratory failure (adjusted HR, 2.35; 95% CI, 1.08-5.11). Participants with HHV-6B DNA in BALF exhibited distinct host gene expression signatures, notable for enriched interferon signaling pathways in participants clinically diagnosed with idiopathic pneumonia. These data implicate HHV-6B as a pulmonary pathogen after allogeneic HCT.

2023-12-18 | GSE244210 | GEO

Streptococcus pneumoniae 670-6B

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Human betaherpesvirus 6B

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Pisolithus croceorrhizus strain:6B

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Human betaherpesvirus 6B

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Transcription profiling of A549 cells after Pneumococcus 6B ST90 and TIGR4 infection

Project description:Compared A549 epithelial cells 2 hrs post-challenge with 6B ST90 CC156 lineage F and TIGR4.

2020-11-10 | E-MTAB-9603 | biostudies-arrayexpress

Expression data from the partially synthetic yeasts SynIXR-1D, -6B, -22D, and controls.

Project description:We have replaced the right arm of chromosome IX in Saccharomyces cerevisiae with a synthetic version to generate synIXR haploids. The synthetic chromosome features multiple sequeunce modifications. We analyzed gene expression by microarray analysis in three synIXR haploids (1D, 6B, and 22D) to detect any changes in synIXR transcripts or global compensatory changes. Biological triplicates of three synIXR haploids (1D, 6B, and 22D) and corresponding controls (either BY4741 or BY4742) were grown to mid-log phase and collected for mRNA isolation.

2011-09-13 | E-GEOD-31326 | biostudies-arrayexpress

Next Generation Sequencing to determine HHV-6B Transcriptome in HCT patients with a recent viral reactivation

Project description:Purpose: The goal of this study is to determine the expression profile of HHV-6B in whole blood samples from transplant patients with HHV-6B genomes detected in plasma Methods: Viral mRNA profiles in whole blood samples of different transplant patients were generated by deep sequencing using Illumina Hiseq. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation for U38 expression was performed using TaqMan Results: Hierarchical clustering uncovered systematic detection of U38 mRNA transcripts in whole blood samples from all patients with a detectable HHV-6B reactivation in their plasma Conclusions: Our study represents the first detailed analysis of viral transcriptomes associated with HHV-6B reactivation in whole blood samples generated by RNA-seq technology. Our results show that NGS offers a comprehensive and more accurate qualitative evaluation of mRNA content within a whole blood sample.

2018-09-08 | GSE115533 | GEO

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