Project description:A custome-made 8x15k oligonucleotide limanda limanda microarray (Agilent) comprised of 14919 experimental probes, was used to characterize gene expression profiles of dab hepatocellular adenoma tumours from sites of different pollution status in Irish Sea.
Project description:We report the application of DNA methylation immunoprecipitation coupled with de novo high throughput sequencing for profiling and identifying methylation alterations in liver tumours of un-sequenced flatfish dab (Limanda limanda). We achieved approximately 90 million and 88 million paired-end reads for hepatocellular adenoma (HCA) and corresponding healthy surrounding tissue (S.T) respectively, of which 47,052,820 and 45,008,483 were uniquely mapped. By calculating the fold changes observed between HCA and S.T we identified 1693 CpG island containing regions that are differentially methylated in HCA compared to S.T (fold change >1.5). The identified genes were further annotated for gene name and biological functions. Ingenuity Pathway Analysis demonstrated enrichment of networks and top functions, such as cell-to-cell signalling, cell cycle, DNA replication, cellular assembly and organisation as well as canonical pathways including Wnt/β-catenin signalling, growth hormone signalling and apoptosis signalling associated with the differentially methylated genes in HCA compared to S.T. Finally, our data showed that MeDIP-HTP sequencing achieves substantial overlapping reads for construction of contigs and annotation of the based on closely related species for studying DNA methylation in un-sequenced species.
Project description:Long rough dab (Hippoglossoides platessoides) is an important flatfish fish species in the north Atlantic arctic and sub-arctic marine foodweb that could be vulnerable to contaminant exposure from offshore petroleum related activities. The study was conducted to map transcriptome responses in long rough dab precision cut liver slice (PCLS) culture exposed to benzo[a]pyrene (BaP). BaP is a polyaromatic hydrocarbon (PAH) which is among the most toxic compounds found in crude oil. PCLS culture was performed under 10 µM BaP exposure for 72 h and transcriptome analysis (RNA-seq) analysis was performed to characterize de novo transcriptome of the liver and identify genes responding to BaP exposure.
