JaMurMuri3
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB71134 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Muricea muricata (spiny sea fan) genome assembly, jaMurMuri3, alternate haplotype
| PRJEB71133 | ENA
Project description:Muricea muricata (spiny sea fan), genomic and transcriptomic data
| PRJEB70483 | ENA
Project description:Tail fan tissue of spiny lobster Genome sequencing
| PRJNA521518 | ENA
Project description:Glove and pot for collecting spiny lobsters with and without tail fan necrosis Genome sequencing and assembly
| PRJNA563794 | ENA
Project description:Background. Coral reef communities are undergoing marked declines due to a variety of stressors including climate change, eutrophication, sedimentation, and disease. The sea fan coral, Gorgonia ventalina, is a tractable study system to investigate the hypothesis that stressors compromise immunity and lead to onset of disease. Functional studies in Gorgonia ventalina immunity indicate that several key pathways and cellular responses are involved in response to natural microbial invaders, although to date the functional and regulatory pathways remain largely un-neffectors, the primary line of defense in invertebrates. This study used short-read sequencing (Illumina GAIIx) to identify genes involved in the response of G. ventalina to a naturally occurring Aplanochytrium spp. parasite. Results. De novo assembly of the G. ventalina transcriptome yielded 90,230 contigs of which 40, 142 were annotated. RNA-Seq analysis revealed 210 differentially expressed genes in sea fans exposed to the Aplanochytrium parasite. Differentially expressed genes involved in immunity include pattern recognition molecules, anti-microbial peptides, wound repair, and reactive oxygen species. Gene enrichment analysis indicated eight biological processes were enriched representing 36 genes, largely involved with protein translation and energy production. Conclusions. This is the first report using high-throughput sequencing to characterize the host response of a coral to a natural pathogen. Furthermore, we have generated the first transcriptome for a soft coral species. G. ventalina is a non-model species for which few sequences had been previously described, and we were able to annotate a large number of genes and describe their potential roles in immune function. Expression analysis revealed genes important in invertebrate innate immune pathways, as well as those whose role is previously un-described in cnidarians. This resource will be valuable in characterizing G. ventalina immune response to infection and co-infection of pathogens in the context of environmental change. RNA seq experiment using Illumina GAIIx to compare sea fans exposed to an Aplanochytrium species compared to controls
2012-08-17 | E-GEOD-40169 | biostudies-arrayexpress
Project description:Sea urchins are emblematic marine animals with a rich fossil record and represent instrumental models for developmental biology. As echinoderms, sea urchins display several characteristics that set them apart from other deuterostomes such as their highly regulative embryonic development and their unique pentaradial adult body plan. To determine whether these characteristics are linked to particular genomic rearrangement or gene regulatory rewiring, we introduce a chromosome-scale genome assembly for sea urchin Paracentrotus lividus as well as extensive transcriptomic and epigenetic profiling during its embryonic development. We found that sea urchins show opposite modalities of genome evolution as compared to those of vertebrates: they retained ancestral chromosomal linkages that otherwise underwent mixing in vertebrates, while their intrachromosomal gene order has evolved much faster between sea urchin species that split 60 Myr ago than it did in vertebrates. We further assessed the conservation of the cis-regulatory program between sea urchins and chordates and identified conserved modules despite the developmental and body plan differences. We documented regulatory events underlying processes like zygotic genome activation and transition to larval stage in sea urchins. We also identified a burst of gene duplication in the echinoid lineage and showed that some of these expanded genes are involved in organismal novelties, such as Aristotle's lantern, tube feet, or in the specification of lineages through for instance the pmar1 and pop genes. Altogether, our results suggest that gene regulatory networks controlling development can be conserved despite extensive gene order rearrangement.
2023-02-09 | GSE202034 | GEO
Project description:FAN (Factor associated with neutral sphingomyelinase activation) is an adaptor protein that constitutively binds to TNF-R1. Microarray analysis was performed in fibroblasts derived from wild-type or FAN knockout mouse embryos to evaluate the role of FAN in TNF-induced gene expression. We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process. Experiment Overall Design: MEFs were derived from C57BL/6 embryos that were either wild type or FAN-/-. Cells were either grown in DMEM 0%FCS for 24h or DMEM 0% FCS for 8h followed by incubation in DMEM 0% FCS containing 50ng/ml TNF for 16h. These four conditions were each used to generate total RNA (RNeasy MidiKit, Qiagen) which was sent to AROS applied biotechnology (Sweden) for Affymetrix GeneChip Mouse Genome 430 2.0 Array analysis.
2009-09-04 | E-GEOD-12275 | biostudies-arrayexpress