Project description:As marine invertebrates, scallops lack adaptive immunity and employ innate immunity as the front line and almost the solo defense mechanism to protect them against invaders. Accumulating research achievements demonstrated that exosomes could act as innate immune effectors that contribute to host defense mechanism. To better understand the immune functions of exosomes in Chlamys farreri, miRNA profiles of hemocytes from scallops injected with PBS, with normal exosomes and LPS stimulating exosomes, respectively, were generated by deep sequencing, in triplicate.
Project description:Global warming and human activities have led to an increased frequency of hypoxia in coastal regions. Hypoxia not only affects the growth and development of scallops but can also cause death, posing a significant challenge to the health and sustainability of aquaculture. Its effects on scallop growth and immune system have been widely reported, but studies on the effects of hypoxic stress on the metabolism of Yesso scallop Mizuhopecten yessoensis are not fully understood. Additionally, the molecular mechanisms of hypoxic stress on damage to the Yesso scallop are still limited. In this study, we deploy high-throughput RNA sequencing (RNA-Seq) and non-targeted liquid chromatography-mass spectrometry (LC-MS) based metabolomics analysis to investigate the alterations in key genes and metabolites in scallops after 24 hours of hypoxia stress (DO: 1 ± 0.1 mg/L). A total of 704 differentially expressed genes (DEGs) and 302 differentially expressed metabolites (DEMs) were identified in the gill tissues of Yesso scallops under hypoxic conditions, respectively. DEGs and DEMs were involved in energy metabolism, antioxidant responses, immune responses, and inflammatory responses, as well as processes of cell apoptosis and cell proliferation. KEGG enrichment analysis shows that the mTOR signaling pathway is a significantly enriched pathway shared by DEGs and DEMs. These findings suggest that Yesso scallops cope with acute hypoxic stress by changing energy metabolism, inhibiting cell apoptosis and proliferation, and increasing immune defense strategies. Overall, the results of this study provide a new understanding of how Yesso scallops respond to hypoxia and provide target genes for the selection and breeding of low-oxygen-tolerant scallops.
Project description:QN Orange scallop was interspecific hybrids with orange adductor muscles. Previous studies shown the accumulation of carotenoids was present in QN Orange scallops. In this study, analysis of miRNA expression profiles was performed to explore possibly regulatory patterns in carotenoid accumulation in adductor muscles of QN Orange scallops. Based on small RNA sequencing, a total of 3289 miRNAs and 91 differential expression miRNAs were identified between white and orange adductor muscles, respectively. GO and KEGG enrichment analysis of target genes of DE miRNA enriched in the transmembrane transporter activity-related pathways, kinase activity-related pathways, signal transduction-related pathways, ABC transporters, Retinol metabolism, lipid related metabolism and calcium signaling pathway.
Project description:As marine invertebrates, scallops lack adaptive immunity and employ innate immunity as the front line and almost the solo defense mechanism to protect them against invaders. Accumulating research achievements demonstrated that exosomes could act as innate immune effectors that contribute to host defense mechanism. To better understand the immune functions of exosomes in Chlamys farreri, mRNA profiles of hemocytes from scallops injected with PBS, with normal exosomes and LPS stimulating exosomes, respectively, were generated by deep sequencing, in triplicate.
Project description:The utility of RADseq in an experimental setting is also demonstrated, based on our chasacterisation of an APOBEC mutation signature in an APOBEC3A transfected mouse cell line. 0D5 cells, derived from SSM3 cells, were co-transfected with a mixture containing pcDNA3.1 vectors expressing either APOBEC3A or APOBEC3B (kindly donated by Vincent Caval), pcDNA3.1 construct expressing deaminase null APOBEC3A linked to a uracil deglycosylase construct and a plasmid encoding mutant GFP and WT mCherry that is a reporter for APOBEC mutagenesis. Cells were grown, and gDNA extracted, prior to preparation of RADseq libraries using a PstI- MspI double-digest. Libraries underwent a Pippin Prep to select fragments in the size range of 220-520 bp (genomic sequence plus 148 bp of adapters). Single-end sequencing (1x101bp) was performed on an Illumina NovaSeq6000 utilizing v1.5 chemistry. Reads were aligned to mm10 using bwa mem and variants called using the GATK4 pipeline.
2023-06-30 | GSE234146 | GEO
Project description:Sequencing data (RADseq, RNAseq) of European whitefish from Lake Constance
| PRJNA497182 | ENA
Project description:Sequencing data (RADseq) for single nucleotide polymorphisms in colour variable European fire salamanders