Project description:Deep Sequencing of mRNA from Drosophila melanogaster, Drosophila Sechellia, and their F1 hybrid. These data were generated in a study to analyze the extent and specificity of trans-splicing in Drosophila. mRNA-seq libraies were prepared from poly(A)+ RNA prepared from whole F1 hybrids of D. melanogaster and D. sechellia (female 0-3d post eclosion). Separate control libraries were prepared from D. melanogaster and D. sechellia total RNA (mixed before library preparation). The results of this study identified 80 novel trans-splicing events between homologous alleles of the same gene. Keywords: RNA-Seq Keywords: Expression profiling by high throughput sequencing
Project description:Purpose: To uncover immune mediated genes and pathways by Pseudomonas aeruginosa infection that are modulated by the homeodomain PITX1/UNC-30, which plays a vital role in the GABAergic signaling in C. elegans Methods: RNA was extracted from synchronized Pseudomonas aeruginosa infected L4 stage unc-30(ok613) and WT using Qiagen extraction kits and following standard methods. The animals were grown on OP50 at 20 C and infected at 25 C. Results: RNA seq analyses shows enriched and signficant Pseudomonas aeruginosa mediated upregulated immune, neuropeptide and metabolism genes and pathways that are dependent of GABAergic signaling Conclusions: Our study uncovered GABAgergic signaling to be modulator of the innate immunity in C elegans during Pseudomonas aeruginosa infection
Project description:Purpose: The goal of this RNA-Seq is to analyze the whole-body transcriptomes from mock-infected bvs oral P.e. infected flies to identify differentially expressed genes Abstract from associated manuscript: When infected by intestinal pathogenic bacteria, animals initiate both local and systemic defence responses. These responses are required to reduce pathogen burden but also to alter host physiology and behaviour to promote infection tolerance, and they are mediated through alterations in host gene expression. Here, we have used transcriptome profiling to examine gene expression changes induced by enteric infection with the gram-negative bacteria Pseudomonas entomophila (P.e) in adult female Drosophila. We find that infection induces a strong upregulation of metabolic gene expression, including gut and fat body-enriched genes involved in lipid transport, lipolysis, and beta-oxidation, as well as glucose and amino acid metabolism genes. Furthermore, we find that the classic innate immune deficiency (Imd)/Relish/NF-KappaB pathway is not required for, and in some cases limits, these infection-mediated increase in metabolic gene expression. We also see that enteric infection with P.e. down regulates the expression of many transcription factors and cell-cell signaling molecules, particularly those previously shown to be involved in gut-to-brain and neuronal signaling. Moreover, as with the metabolic genes, these changes occurred largely independent of the Imd pathway. Together, our study identifies many metabolic, signaling and transcription factor gene expression changes that may contribute to organismal physiological and behavioural responses to enteric pathogen infection. Results: RNA Seq differential expression analysis identified a significant (p<0.05,> 1.5 fold expression) change in 2835transcripts, with 1602 transcripts showing reduced expression levels and 1233 transcripts with elevated expression levels.
Project description:Purpose: The goal of this study is to compare NGS-derived Arabidopsis thaliana transcriptome profiling (RNA-Seq) obtained from tissues infected with a variety of Pseudomonas syryingae effector mutants to better understand their impact on their host's transcriptional program. We report the application of RNA-sequencing technology (Illumina Hi-Seq) for high-throughput profiling Arabidopsis thaliana transcriptomes upon infection with the model pathogen Pseudomonas syringae (wild-type and mutants).
Project description:In our study, we used a mouse model infected with Pseudomonas aeruginosa (PA) to provoke a painful, sight-threatening corneal infection. FACS sorted WT and Gal-8-/- neutrophils of PA infected corneas were processed for next-generation transcriptomic RNA sequencing (RNA-seq).
Project description:Data analysis is a critical part of quantitative proteomics studies in interpreting biological questions. Numerous computational tools including protein quantification, imputation, and differential expression (DE) analysis were generated in the past decade. However, searching optimized tools is still an unsolved issue. Moreover, due to the rapid development of RNA-Seq technology, a vast number of DE analysis methods are created. Applying these newly developed RNA-Seq-oriented tools to proteomics data is still a question that needs to be addressed. In order to benchmark these analysis methods, a proteomics dataset constituted the proteins derived from human, yeast, and drosophila with different ratios were generated. Based on this dataset, DE analysis tools (including array-based and RNA-Seq based), imputation algorithms, and protein quantification methods were compared and benchmarked. This study provided useful information on analyzing quantitative proteomics datasets. All the methods used in this study were integrated into Perseus which are available at https://www.maxquant.org/perseus.
Project description:Drosophila harbor substantial genetic variation for antibacterial defense. We allowed wild-caught Drosophila melanogaster to evolve a defense response to systemic infection with the human opportunistic pathogen, Pseudomonas aeruginosa over 10 generations. We performed genome wide transcriptional profiling in selected lines relative to control lines (not infected, but were exposed to the same bottleneck in population size as their paired selected lines by randomly selecting a set of individuals to found the next generation, and then infected at the end of the 10 generations), to identify specifically the genetic basis of the evolved immune response.
Project description:Samples were collected from infected male patients and RNA seq was used to determine the transcriptome of Neisseria gonorrhoeae both during infection and during growth in chemically defined media (CDM). Samples were also collected from infected female patients to determine the transcriptome differences between male and female infections.