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Genome-wide maps of DNA methylation and gene expression for multiple regions within a breast tumor [RRBS]

ABSTRACT: Genome-wide maps of DNA methylation and gene expression for multiple regions within a breast tumor [RRBS]

PROVIDER: PRJNA510704 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8346120_1.fastq.gz	Fastqsanger.gz
	SRR8346120_2.fastq.gz	Fastqsanger.gz
	SRR8346121_1.fastq.gz	Fastqsanger.gz
	SRR8346121_2.fastq.gz	Fastqsanger.gz
	SRR8346122_1.fastq.gz	Fastqsanger.gz

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Genome-wide maps of DNA methylation and gene expression for multiple regions within a breast tumor [RRBS]

Project description:As the differentiation state of the cells is affected by epigenetic modification regulation, the abnormal epigenetic modification is an important factor leading to the intratumoral heterogeneity. To further understand of the intratumoral epigenetic heterogeneity, we performed Reduced Representation Bisulfite Sequencing and RNA sequencing for multiple regions within a breast tumor and exhibited the epigenetic maps of different regions. We detected intratumoral heterogeneity-related molecular features and further explored the correlation between tumor heterogeneity and tumor hypoxic microenvironment.

2020-01-01 | GSE124027 | GEO

Genome-wide maps of DNA methylation and gene expression for multiple regions within a breast tumor [RNA-Seq]

2020-01-01 | GSE124030 | GEO

Genome-wide maps of DNA methylation and gene expression for multiple regions within a breast tumor

Project description:Genome-wide maps of DNA methylation and gene expression for multiple regions within a breast tumor

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Genome-wide maps of DNA methylation and gene expression for multiple regions within a breast tumor [RNA-Seq]

Project description:Genome-wide maps of DNA methylation and gene expression for multiple regions within a breast tumor [RNA-Seq]

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DNA methylation analysis by RRBS in germ cells of mice exposed to Vinclozolin

2015-06-22 | GSE65784 | GEO

Polygenic trait SNPs in noncoding genomic regions: using chromatin maps to elucidate potential regulatory mechanisms in blood pressure [RNA-seq]

Project description:Many polygenic traits are associated with hundreds of single nucleotide polymorphisms (SNPs), which predominantly (>95%) reside within noncoding genomic regions, making it difficult to understand how they regulate complex traits, such as blood pressure (BP). Given the central role of the kidney in regulating BP, we hypothesized that chromatin-accessible regions in renal tissue would be enriched for BP-associated SNPs (bpSNPs). We developed chromatin state and transcriptomic maps of the proximal tubules (PT) and medullary thick ascending limbs (mTAL) isolated from humans and rats. These maps revealed shared cis-regulatory elements (CREs) across humans and rats, including upstream transcriptional regulators. Notably, bpSNPs were significantly enriched within open chromatin regions, suggesting they potentially alter the activity of CREs and near genes critical to renal development and function. Collectively, this work lays a foundation for interrogating how intergenic SNPs may regulate polygenic traits such as BP.

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DNA methylation analysis by RRBS in germ cells of mice exposed to Vinclozolin

Project description:We provide quantitative maps of cytosine methylation at single base resolution by RRBS in E13.5 primordial germ cells and adult sperm purified from mice exposed to Vinclozolin. Pregnant F0 female mice were exposed to two doses (a low dose VD1=1 mg/kg bw/d and a high dose VD2=100mg/kg bw/d) of Vinclozolin in the drinking water during pregnancy. We isolated primordial germ cells at E13.5 and mature sperm from adult F1 males obtained from control and exposed mothers. For PGCs, we sequenced RRBS libraries prepared from one pool isolated from F1 embryos exposed to the low dose, one pool isolated from F1 embryos exposed to the high dose, and two control pools isolated from unexposed embryos. For sperm, we sequenced three RRBS libraries prepared from a pool of sperm isolated from F1 males exposed to the high dose, and five RRBS libraries prepared from control pools isolated from unexposed animals.

2015-06-22 | E-GEOD-65784 | biostudies-arrayexpress

The transcriptomic data of multiple brain regions in mice

Project description:The transcriptomic data of multiple brain regions in mice

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Rapid and affordable genome-wide bisulfite DNA sequencing by XmaI-RRBS

Project description:We describe XmaI-RRBS method for rapid and affordable genome-wide DNA methylation analysis, with library preparation taking only four days and sequencing possible within four hours. Small sizes of the XmaI-RRBS libraries allow their multiplexing and sequencing on the benchtop high-throughput machines. Described here is the first RRBS protocol validated for the Ion Torrent Personal Genome Machine. DNA from MCF7 cell line and 6 normal breast samples (total 7 samples) were subjected to reduced representation bisulfite sequencing analysis (XmaI-RRBS) by using Ion Torrent platform.

2015-11-01 | E-GEOD-74126 | biostudies-arrayexpress

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