Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Limanda limanda

ABSTRACT: DNA methylation profiling of flatfish dab (Limanda limanda)

PROVIDER: PRJNA144935 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR326300.fastq.gz	Fastqsanger.gz
	SRR326301_1.fastq.gz	Fastqsanger.gz
	SRR326301_2.fastq.gz	Fastqsanger.gz
	SRR326302.fastq.gz	Fastqsanger.gz
	SRR326303_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

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

fLimLim

Project description:Limanda limanda (common dab)

| PRJEB65388 | ENA

Transcription profiling of dab hepatocellular adenoma liver tumours (Limanda limanda)

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

fLimLim1

Project description:Limanda limanda (common dab) genome assembly, fLimLim1

| PRJEB68099 | ENA

fLimLim

Project description:Limanda limanda (common dab), genomic and transcriptomic data

| PRJEB65387 | ENA

fLimLim1 alternate haplotype

Project description:Limanda limanda (common dab) genome assembly, fLimLim1, alternate haplotype

| PRJEB68100 | ENA

Transcriptome analysis of long rough dab (Hippoglossoides platessoides) liver slice culture exposed to benzo[a]pyrene.

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.

2024-09-09 | E-MTAB-13932 | biostudies-arrayexpress

Transcriptional profiling of flatfish (Solea senegalensis) spermatogenesis

Project description:This SuperSeries is composed of the following subset Series: GSE21634: Transcriptional profiling of flatfish (Solea senegalensis) spermatogenesis_1 GSE21635: Transcriptional profiling of flatfish (Solea senegalensis) spermatogenesis_2 GSE21637: Transcriptional profiling of flatfish (Solea senegalensis) spermatogenesis_3 Refer to individual Series

2010-05-07 | E-GEOD-21694 | biostudies-arrayexpress

Limanda limanda

Project description:Limanda limanda overview

| PRJNA158215 | ENA

DNA methylation dynamics associated with visual system remodeling during flatfish metamorphosis

Project description:DNA methylation dynamics associated with visual system remodeling during flatfish metamorphosis

| PRJNA1234131 | ENA