DdRADseq analysis of a hybrid swarm
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PROVIDER: PRJEB24320 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The puropose of this experiment was to identify gene expression changes that result from 5-aza-2-deoxycytidine induced DNA demethylation of Swarm rat chondrosarcoma cells. The gene expression profiles of untreated Swarm rat chondrosarcoma cells were compared to the gene expression profiles of Swarm rat chondrosarcoma cells that were treated for 5 passages with a low dose of 5-aza-2-deoxycytidine (0.1uM). Five chip study. For these experiments, microarray was carried out on untreated (control) Swarm rat chondrosarcoma cells (3 biological replicates), and microarray was also carried out on Swarm rat chondrosarcoma cells treated with 5-aza-2-deoxycytidine (2 biological replicates).
2010-08-06 | E-GEOD-17598 | biostudies-arrayexpress
Project description:The puropose of this experiment was to identify gene expression changes that result from 5-aza-2-deoxycytidine induced DNA demethylation of Swarm rat chondrosarcoma cells. The gene expression profiles of untreated Swarm rat chondrosarcoma cells were compared to the gene expression profiles of Swarm rat chondrosarcoma cells that were treated for 5 passages with a low dose of 5-aza-2-deoxycytidine (0.1uM).
2010-08-06 | GSE17598 | GEO
Project description:Non-additive gene regulation has been recently suggested as an important factor promoting phenotypic variation and plasticity. In order to obtain a description of gene expression status at an early stage of ear development in a maize (Zea mays L.) F1 hybrid as relative to its parental inbreds, we compared gene expression profiles in immature ears of elite inbred lines B73 and H99 to one of their F1 hybrids (B73xH99) using cDNA microarray technology. Results show several genes expressed at a significantly different level between both inbred lines and their hybrid. In addition, gene expression non-additivity in the hybrid was detected on a broad scale, consisting of both dominance and over-dominance components, indicating that complex non-additive interactions at the molecular level exist in the developing ear of the studied maize hybrid. Non-additively regulated genes belong to a wide range of molecular functions, indicating that several regulatory and metabolic patterns are possibly affected during ear development in the investigated hybrid. We discuss the possibility that observed gene expression non-additivity in immature ear might be an early molecular manifestation of hybrid vigor, the most exploited factor for maize agronomic improvement.
2007-10-01 | GSE2771 | GEO
Project description:The aim of this project is to promote the breath volatile marker concept for colorectal cancer (CRC) screening by advancing developing the application of a novel hybrid analyzer for the purpose.
The hybrid analyzer concept is expected to benefit of combining metal-oxide (MOX) and infrared spectrum (IR) sensor acquired data. The current study will be the first globally to address this concept in CRC detection. In addition, traditional methods, in particular, gas chromatography coupled to mass spectrometry (GC-MS) will be used to address the biological relevance of the VOCs emission from cancer tissue and will assist in further advances of the hybrid-sensing approach.
| 2399547 | ecrin-mdr-crc
Project description:Movement of food-borne pathogens on moist surfaces enables them to migrate towards more favorable niches and facilitate their survival for extended periods of time. Salmonella enterica serovar Typhimurium mutants defective in OPG synthesis are unable to exhibit motility on moist surfaces (swarming) however their mobility in liquid (swim motility) remains unaffected. In order to understand the role of OPG in swarm motility, transcriptomic analysis was performed using cells growing on a moist agar surface. In the opgGH-deletion mutant, lack of OPG significantly altered transcription of 1039 genes out of total 4712 genes (22%). Introduction of a plasmid borne copy of opgGH into the opgGH-deletion mutant restored normal expression of all but 30 genes, indicating a wide-range influence of OPG on gene expression under the swarm motility condition. Major pathways that were differentially-expressed in opgGH mutants were motility, virulence and invasion, and genes related to the secondary messenger molecule, cyclic di-GMP. These observations provide insights and help explain the pleiotropic nature of OPG mutants such as sub-optimal virulence and competitive organ colonization in mice, biofilm formation, and sensitivity towards detergent stress.
2019-08-31 | GSE86311 | GEO
Project description:A resident of animal intestines, Proteus mirabilis is a major cause of catheter-associated urinary tract infections and can cause recurrent, persistent infections. Swarming, which is a collective behavior that promotes centimeter-scale population migration, is implicated in colonization of bladders and kidneys. A regulatory factor of swarming is kin recognition, which involves the transfer of a self-identity protein from one cell into a physically adjacent neighboring cell. However, how kin recognition regulates swarming was previously unclear. We have now shown a mechanism linking kin recognition, swarm migration, and antibiotics tolerance: cells induce a transient antibiotics-tolerant, persister-like state in adjacent non-identical cells which in turn prevents non-identical cells from continuing to participate in collective swarming. These affected non-identical cells continue to exhibit large-scale gene expression suggesting an active shift into a different expression state. These data provide two key insights for the field. First, kin recognition can be a regulatory mechanism that acts with spatial and temporal precision. Second, induction into an antibiotics-tolerant state, instead of occurring stochastically, can be physically and spatially regulated by neighboring cells. These insights highlight the importance of further developing four-dimensional (time and X-, Y-, Z-axes) model systems for interrogating cell-cell signaling and control in microbial populations.
2019-05-23 | GSE131647 | GEO
Project description:Non-additive gene regulation has been recently suggested as an important factor promoting phenotypic variation and plasticity. In order to obtain a description of gene expression status at an early stage of ear development in a maize (Zea mays L.) F1 hybrid as relative to its parental inbreds, we compared gene expression profiles in immature ears of elite inbred lines B73 and H99 to one of their F1 hybrids (B73xH99) using cDNA microarray technology. Results show several genes expressed at a significantly different level between both inbred lines and their hybrid. In addition, gene expression non-additivity in the hybrid was detected on a broad scale, consisting of both dominance and over-dominance components, indicating that complex non-additive interactions at the molecular level exist in the developing ear of the studied maize hybrid. Non-additively regulated genes belong to a wide range of molecular functions, indicating that several regulatory and metabolic patterns are possibly affected during ear development in the investigated hybrid. We discuss the possibility that observed gene expression non-additivity in immature ear might be an early molecular manifestation of hybrid vigor, the most exploited factor for maize agronomic improvement. We directly contrasted both B73 and H99 inbred lines vs. their F1 heterotic hybrid transcriptomes in immature ear. Our experimental design consisted of 10 cDNA microarray hybridizations, 5 for each combination of hybrid vs. inbred genotypes, involving 20 separate labeling reactions. Labeling dyes were swapped in two of the five replicates for each combination. In each hybridization, control channel was assigned to the F1 hybrid, and differences in transcriptional levels between B73 and H99 were inferred using the hybrid as a common reference sample in an indirect experimental design. To take in account variability in transcript population among individuals, total RNA coming from different isolations, each collected on multiple individuals, were mixed before poly(A+) RNA purification. All hybridizations on microarray slides were then performed using cDNA independently labeled from the poly(A+) RNA purification product for each genotype. Base-two logarithms of expression ratios were subjected to one-class response significance analysis in SAM v. 2.20 software [Tusher et al. 2001]. For each EST the estimates of additive parameter "a" and dominance parameter "d" (middle-parent heterosis) were obtained as a = (L2 – L1)/2 d = (L1 + L2)/2 (where L1 and L2 are mean base-two logarithms of expression ratios of F1 vs. B73 and F1 vs. H99, respectively). Positive values of "a" indicate expression values bigger in B73 than in H99. The dominance/additivity ratio (d/|a|) was also calculated [Falconer 1989]. Evaluation of statistical significance of parameters was done by calculating standard errors of the estimates "a" and "d" as standard errors of linear functions of the means. Significance testing was done correspondingly, using an F-test for linear contrasts. P-values for the families of tests corresponding to each parameter were subjected to global error analyses using a method based on fitting mixture distribution [Allison et al. 2002], allowing to estimate the false discovery rates (FDR) and false negative rates (FNR). Confidence intervals for d/|a| ratios were obtained by Fieller’s method [Piepho and Emrich 2005], allowing to classify the genes into different dominance type classes.
2007-10-01 | E-GEOD-2771 | biostudies-arrayexpress
Project description:F1 hybrids can outperform their parents in yield and vegetative biomass, features of hybrid vigor which form the basis of the hybrid seed industry. The yield advantage of the F1 is lost in the F2 and subsequent generations. In Arabidopsis, from F2 plants which have a F1 –like phenotype, we have by recurrent selection produced pure breeding F5/F6 lines “Hybrid Mimics”, in which the characteristics of the F1 Hybrid are stabilized. These Hybrid Mimic lines, like the F1 Hybrid, have larger leaves than the parent plant, the leaves having increased photosynthetic cell numbers, and in some lines increased size of cells, suggesting an increased supply of photosynthate. A comparison of the differentially expressed genes in the F1 Hybrid with those of eight Hybrid Mimic lines has identified metabolic pathways altered in both; these pathways include down regulation of defense response pathways and altered abiotic response pathways. F6 Hybrid Mimic lines are mostly homozygous at each locus in the genome yet retain the large F1-like phenotype. Many alleles in the F6 plants, when they are homozygous, have expression levels different to the level in the parent. We consider this altered expression to be a consequence of trans-regulation of genes from one parent by genes from the other parent. Transregulation could also arise from epigenetic modifications in the F1. The pure breeding Hybrid Mimics have been valuable in probing the mechanisms of hybrid vigor and may also prove to be useful hybrid vigor equivalents in agriculture.
2015-08-17 | GSE64742 | GEO
Project description:F1 hybrids can outperform their parents in yield and vegetative biomass, features of hybrid vigor which form the basis of the hybrid seed industry. The yield advantage of the F1 is lost in the F2 and subsequent generations. In Arabidopsis, from F2 plants which have a F1 –like phenotype, we have by recurrent selection produced pure breeding F5/F6 lines “Hybrid Mimics”, in which the characteristics of the F1 Hybrid are stabilized. These Hybrid Mimic lines, like the F1 Hybrid, have larger leaves than the parent plant, the leaves having increased photosynthetic cell numbers, and in some lines increased size of cells, suggesting an increased supply of photosynthate. A comparison of the differentially expressed genes in the F1 Hybrid with those of eight Hybrid Mimic lines has identified metabolic pathways altered in both; these pathways include down regulation of defense response pathways and altered abiotic response pathways. F6 Hybrid Mimic lines are mostly homozygous at each locus in the genome yet retain the large F1-like phenotype. Many alleles in the F6 plants, when they are homozygous, have expression levels different to the level in the parent. We consider this altered expression to be a consequence of trans-regulation of genes from one parent by genes from the other parent. Transregulation could also arise from epigenetic modifications in the F1. The pure breeding Hybrid Mimics have been valuable in probing the mechanisms of hybrid vigor and may also prove to be useful hybrid vigor equivalents in agriculture.
2015-08-17 | GSE64740 | GEO