Project description:Transcriptional profiling of NHDF Cells comparing control untreated fibroblasts with fibroblasts coincubated with three different species of the Borrelia burgdorferi sensu lato group.
2016-05-22 | GSE77058 | GEO
Project description:WGS Bacillus cereus sensu lato
Project description:Transcriptional control of gene expression is a result of complex interactions between the cis-regulatory elements (CRE) at gene promoters. To understand the regulatory logic of a cell, we need to identify the CRE combinations that regulate gene expression. We developed a sensitive computational method to identify phylogenetically conserved CRE combinations for any species of interest. In contrast to previous methods, we do not need to align genomes to identify these combinations. We applied the method in 7 sensu stricto and sensu lato Saccharomyces species. 80% of the predictions displayed some evidence of combinatorial transcriptional behavior in several existing datasets including 1) ChIP-chip data for co-localization of transcription factors, 2) gene expression data for co-expression of predicted regulatory targets, and 3) gene ontology databases for common pathway membership of predicted regulatory targets. To establish definitive evidence that these CRE interactions influence TF occupancy, we performed ChIPseq experiments on transcription factors in a wild-type strain and strains in which a predicted cofactor was deleted. Our experiments showed that TF occupancy at the promoters of the CRE combination target genes depends on the predicted cofactor while occupancy of other promoters is independent of the predicted cofactor. ChIP-seq of 6 myc-tagged Transcription factors in wild-type and predicted co-factor knockout yeast strains in triplicate
Project description:The parasite species complex Anisakis simplex sensu lato (Anisakis simplex sensu stricto; (A. simplex s.s.), A. pegreffii, A. simplex C) is the main cause of severe anisakiasis (allergy) worldwide and is now an important health matter. In this study, the relationship of this Anisakis species complex and their allergenic capacities is assessed by studying the differences between the two most frequent species (A. simplex s.s., A. pegreffii) and their hybrid haplotype by studying active L3 larvae parasiting Merluccius merluccius.
Project description:Seaweeds in the upper intertidal zone experience extreme desiccation during low tide, followed by rapid rehydration during high tide. Porphyra sensu lato are typical upper intertidal seaweeds. Thus, it is valuable to investigate the adaptive conditions and mechanisms of seaweed to desiccation-rehydration stress.
Project description:Transcriptional control of gene expression is a result of complex interactions between the cis-regulatory elements (CRE) at gene promoters. To understand the regulatory logic of a cell, we need to identify the CRE combinations that regulate gene expression. We developed a sensitive computational method to identify phylogenetically conserved CRE combinations for any species of interest. In contrast to previous methods, we do not need to align genomes to identify these combinations. We applied the method in 7 sensu stricto and sensu lato Saccharomyces species. 80% of the predictions displayed some evidence of combinatorial transcriptional behavior in several existing datasets including 1) ChIP-chip data for co-localization of transcription factors, 2) gene expression data for co-expression of predicted regulatory targets, and 3) gene ontology databases for common pathway membership of predicted regulatory targets. To establish definitive evidence that these CRE interactions influence TF occupancy, we performed ChIPseq experiments on transcription factors in a wild-type strain and strains in which a predicted cofactor was deleted. Our experiments showed that TF occupancy at the promoters of the CRE combination target genes depends on the predicted cofactor while occupancy of other promoters is independent of the predicted cofactor.