Project description:Analysis of transcriptome in a strand-specific manner to further refine previous genome annotation; RNA-seq was also combined with microarray and proteome analysis to further define the S. Typhi ompR regulon and identify novel ompR regulated transcripts.
2009-03-03 | E-TABM-644 | biostudies-arrayexpress
Project description:RNA-seq profiling of Fugacium kawagutii reveals strong metabolic response to and impacts on symbiosis potential of iron deficiency and other trace metals
| PRJNA550184 | ENA
Project description:Physiological and transcriptomic responses to N-deficiency and ammonium: nitrate shift in Fugacium kawagutii (Symbiodiniaceae)
| PRJNA630740 | ENA
Project description:Novel plastid genome characteristics in Fugacium kawagutii and accelerated evolution of plastid proteins in dinoflagellates
Project description:Muscles undergo developmental transitions in gene expression and alternative splicing that are necessary to refine sarcomere structure and contractility. CUG-BP and ETR-3-like (CELF) family RNA binding proteins are important regulators of RNA processing during myogenesis that are misregulated in diseases such as myotonic dystrophy (DM1). In this work we report a function for Bruno 1 (Bru1, Arrest), a CELF1/2 family homolog in Drosophila, during early muscle myogenesis as well as during later stages of sarcomere assembly and myofiber maturation. We identify an imbalance in growth in sarcomere length and width during later stages of development as the mechanism driving abnormal radial growth, myofibril fusion and the formation of hollow myofibrils in bru1 mutant muscle. Molecularly, we characterize a genome-wide transition from immature to mature sarcomere gene isoform expression in flight muscle development that is blocked in bru1 mutants. We performed whole proteome mass spectrometry in control and bru1 mutant muscle to identify changes to the proteome, and correlated these changes to gene expression and exon use gleaned from mRNA-Seq. Our results reveal the conserved nature of CELF function in regulating cytoskeletal dynamics in muscle development, and demonstrate that defective RNA processing due to misexpression of CELF proteins causes wide-reaching structural defects and progressive malfunction of affected muscles that cannot be rescued by late-stage gene replacement.
Project description:We conducted the genome-wide mRNA expression profiling in parallel with miRNA expression profiling using RNA samples extracted from rat incisor enamel organs, so as to refine the number of predicted gene targets for miRNA regulators.
Project description:This SuperSeries is composed of the following subset Series: GSE38356: The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts [RNA-seq] GSE38201: The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts [PAR-CLIP] GSE38355: The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts [protein occupancy profiling] Refer to individual Series
Project description:We conducted the genome-wide lncRNA and mRNA expression profiling using RNA samples extracted from rat incisor enamel organs, so as to refine the number of predicted gene targets for lncRNA regulators.
Project description:Samples are from a screening experiment on 5 laboratory cultures of the coral endosymbiont: Symbiodiniaceae (Symbiodinium linuchae, Breviolum psygmophilum, Durusdinium trenchii, Effrenium voratum and Fugacium kawagutii). Samples are also from a thermal stress experiment (increased temperatures from 26 to 32 degrees C) carried out on Durusdinium trenchii and Cladocopium goreaui, two common coral endosymbionts on the Great Barrier Reef. All samples were collected on Markes Tenax TA thermal desorption tubes.
Lawson, C.A., Possell, M., Seymour, J.R., Raina, J.B. and Suggett, D.J., 2019. Coral endosymbionts (Symbiodiniaceae) emit species-specific volatilomes that shift when exposed to thermal stress. Scientific reports, 9(1), pp.1-11.
