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Reduced representation bisulfite sequencing (RRBS) of brown adipose tissue from postnatal day 12 mice perinatally exposed to vehicle or DDT

ABSTRACT: Reduced representation bisulfite sequencing (RRBS) of brown adipose tissue from postnatal day 12 mice perinatally exposed to vehicle or DDT

PROVIDER: PRJNA1074053 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27896000.fastq.gz	Fastqsanger.gz
	SRR27896100.fastq.gz	Fastqsanger.gz
	SRR27896001.fastq.gz	Fastqsanger.gz
	SRR27896101.fastq.gz	Fastqsanger.gz
	SRR27896002.fastq.gz	Fastqsanger.gz

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Reduced representation bisulfite sequencing (RRBS) of brown adipose tissue from postnatal day 12 mice perinatally exposed to vehicle or DDT

Project description:The insecticide dichlorodiphenyltrichloroethane (DDT) and its persistent metabolite, dichlorodiphenyldichloroethylene (DDE), have been associated with increased adiposity and obesity in rodent and human studies. These lipophilic pollutants accumulate in adipose tissue and it is theorized that their exposure leads to decreased decrease energy expenditure through the impairment of thermogenesis in brown adipose tissue. We hypothesized that impaired thermogenesis is due to persistent epigenetic modifications of brown adipose tissue. To address this, we exposed C57BL/6J mice to DDT from gestational day 11.5 to postnatal day 5 and isolated brown adipose tissue for RRBS from one offspring per litter when mice reached postnatal day 12 (n=20 DDT litters and 22 vehicle litters). DNA methylation levels in brown adipose tissue of mice perinatally exposed to vehicle or DDT were determined using RRBS. Analyses of differential methylation and KEGG pathway enrichment were performed.

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High concordance between Illumina HiSeq2500 and NextSeq500 for Reduced Representation Bisulfite Sequencing (RRBS)

Project description:Reduced representation bisulfite sequencing (RRBS) provides an efficient method for measuring DNA methylation at single base resolution in regions of high CpG density. This technique has been extensively tested on the HiSeq2500, which uses a 4-colour detection method, however it is unclear if the method will also work on the NextSeq500 platform, which employs a 2-colour detection system. We created an RRBS library and sequenced it on both the HiSeq2500 and NextSeq500, and found no significant difference in the base composition of reads derived from either machine. Moreover, the methylation calls made from the data of each instrument were highly concordant, with methylation patterns across the genome appearing as expected. Therefore, RRBS can be sequenced on the Nextseq500 with comparable quality to that of the HiSeq2500.

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Project description:DNA methylation is an important regulatory mechanism that contributes to transcriptional repression. To examine whether DNA methylation affects the transcriptional changes of DNA repair genes under H2O2-induced oxidative stress, we performed reduced representation bisulfite sequencing (RRBS) in H2O2-treated and untreated HCT116 cells.

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Project description:Reduced representation bisulfite sequencing (RRBS) of cultured cells derived from Parkinson's disease patient [RRBS-seq]

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