Transciptional profile of a M. smegmatis mc2155 ΔsigF strain under standard growth conditions
ABSTRACT: Comparing transciptional profile of a M. smegmatis mc2155 ΔsigF strain and wild type (control) in in vitro culture at two time points (exponential phase and stationary phase) for identification of SigF-dependent genes. Analysis of 2 time points: exponential and stationary phase. 4 biological replicates comparing expression of wild type (control) and ΔsigF strain incl. dye swaps for each time point. 3 technical replicates per array
SigF is an alternative sigma factor that is highly conserved among species of the genus Mycobacterium. In this study we identified the SigF regulon in Mycobacterium smegmatis using whole-genome microarray and promoter consensus analyses. In total, 64 genes in exponential phase and 124 genes in stationary phase are SigF dependent (P < 0.01, >2-fold expression change). Our experimental data reveal the SigF-dependent promoter consensus GTTT-N((15-17))-GGGTA for M. smegmatis, and we propose 130 pote ...[more]
Project description:Transcriptional profiling of M. smegmatis MB100pruR vs. MB100 (isogenic parent) grown in serumvials on Hartmans de Bont medium supplemented with glycerol and proline Two-condition experiment. Biological replicates: 4 independently grown and harvested. One replicate per array.
Project description:Transcriptional profiling of M. smegmatis mc2155 grown on Hartmans de Bont (HdB) supplemented with 0.2% glycerol and 0.05% Tween80 challenged with 2 μg/ml Bedaquiline and Dimethyl sulfoxide (DMSO) Two-condition experiment. Biological replicates: 5 independently grown and harvested. One replicate per array.
Project description:To identify the AmtR regulon of Mycobacterium smegmatis, we created a markerless deletion of the amtR gene in the background of strain M. smegmatis mc2155 (wild-type) and compared the transcription profile of both strains grown in batch culture under aerobic conditions on Hartmans de Bont medium supplemented with glycerol (carbon source) and lysine (sole nitrogen source) using microarray. Cells were harvested in early exponential growth stage.
Project description:DosR is the regulator of a two-component system in mycobacteria that senses oxygen concentration and the redox state of the cells. To determine the DosR regulon, the transcriptomes of M. smegmatis mc2155 and the ΔdosR cells were compared by microarray at 10 hours following induction of oxygen-limitation in serum vials. 4 biological replicates incl. 2 dye swaps. 3 technical replicates per array
Project description:Transcriptional profiling of M. smegmatis JR121 expressing VapC and VapBC grown in flasks on Hartmans de Bont medium supplemented with 0.2% glycerol Comparing transcriptional response of strain JR121 to conditional expression of VapC toxin compared with the expression of VapBC complex. Biological replicates: 4 independently grown and harvested. One replicate per array.
Project description:Transcriptional profiling of M. smegmatis and Dcrp1 grown in flasks on Hartmans de Bont medium supplemented with 10 mM glycerol. Transcriptional profiling of M.smegmatis HLA102 harboring tetracycline inducible vector pMind containing the Crp2 and M. smegmatis harboring pMind grown in flasks on Hartmans de Bont medium supplemented with 10 mM glycerol Comparing transcriptional response of wild-type compared with the deletion of crp1 gene (Msmeg_0539). Biological replicates: 4 independently grown and harvested. One replicate per array. Comparing transcriptional response of strain HLA102 to conditional expression of Crp2 (Msmeg_6189) compared with the wild-type with empty vector pMind. Biological replicates: 4 independently grown and harvested. One replicate per array.
Project description:Transcriptional profiling of M. smegmatis grown at 69h doubling time compared to 4.6h doubling time both at 50% air saturation. Transcriptional profiling of M. smegmatis grown at 69h doubling time with 50%, 2.5% and 0.6% air saturation. Two-condition experiment. Biological replicates: 5 independently grown and harvested. One replicate per array.
Project description:The transcription factor complex AP-1 (Activator protein 1) is composed of Jun (c-Jun, JunB, JunD) and Fos proteins (c-Fos, FosB, Fra-1, Fra-2) which control a variety of stress responses, including cell proliferation, apoptosis, inflammation, wound healing, and cancer. Individual Fos proteins have been thoroughly studied in gain- and loss-of-function mouse models, which revealed important functions in bone cell proliferation and differentiation. We have recently demonstrated that loss of Fra-2 causes perinatal lethality and severe osteopenia due to several cellular defects, including a chondrocyte differentiation defect and a control of osteoclast survival and size. Moreover, we have reported a profibrogenic function of Fra-2 in transgenic mice, in which ectopic expression of Fra-2 in various organs resulted in generalized fibrosis with predominant manifestations in the lung. Fra-2 knock-out newborns have increased numbers and size of osteoclasts in vivo. The pulmonary phenotype observed in Fra-2Tg mice is characterized by vascular remodeling and obliteration of pulmonary arteries, which coincides with expression of osteopontin, an AP-1 target gene involved in vascular remodeling and fibrogenesis. These alterations are followed by inflammation; release of profibrogenic factors, such as IL-4, insulin-like growth factor 1, and CXCL5. The expression profiling study was performed to analyse changes in transcript levels in lung over a period of time. Total RNA of four mutant male animals at each time point (age: 6, 10 and 14 weeks) were hybridised versus a pool of total RNA of four wild type mice of the corresponding age. For each mutant animal, two technical chip hybridisations were performed, including a dye-swap experiment (in total, 8 hybridisation of each time point = 2 technical replicates x 4 biological replicates).
Project description:The type III effector (T3E) AWR5 from the phytopathogen Ralstonia solanacearum causes disease in many plants relevant in agriculture. Heterologous expression in yeast of AWR5 from an integrated tetO promoter caused strong growth inhibition. In this series of experiments we investigate the possible changes in the transcriptional profile in a time-course (2, 4 and 6 h) response to AWR5 production. Yeast strains were grown overnight in rich YPD medium with doxycycline 15 µg/ml (repressing conditions), then normalized to OD600=0.05 and grown resumed in YPD+dox (non-inducing conditions) or YPD (inducing conditions). Samples were taken at 2, 4 or 6 hours for each condition. Two biological replicates were made for each time point.
Project description:Recently, expression profiling of breast carcinomas has revealed gene signatures that predict clinical outcome, and discerned prognostically relevant breast cancer subtypes. Measurement of the degree of genomic instability provides a very similar stratification of prognostic groups. We therefore hypothesized that these features are linked. We used gene expression profiling of 48 breast cancer specimens that profoundly differed in their degree of genomic instability and identified a set of 12 genes that defines the two groups. The biological and prognostic significance of this gene set was established through survival prediction in published datasets from patients with breast cancer. Of note, the gene expression signatures that define specific prognostic subtypes in other breast cancer datasets predicted genomic instability in our samples. This remarkable congruence suggests a biological dependency of poor-prognosis gene signatures, breast cancer subtypes, genomic instability, and clinical outcome. Keywords: disease state analysis 44 samples