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.

2011-11-04 | E-MTAB-734 | biostudies-arrayexpress

Limanda limanda

Project description:DNA methylation profiling of flatfish dab (Limanda limanda)

| PRJNA144935 | ENA

DNA methylation profiling of flatfish dab (Limanda limanda)

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/Î²-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.

2011-11-09 | GSE31124 | GEO

Limanda limanda

Project description:Limanda limanda overview

| PRJNA158215 | ENA

fAbrBra

Project description:Abramis brama (common bream), genomic and transcriptomic data

| PRJEB71618 | ENA

ioAesJunc

Project description:Aeshna juncea (common hawker), genomic and transcriptomic data

| PRJEB70646 | ENA

bGalChl

Project description:Gallinula chloropus (common moorhen), genomic and transcriptomic data