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

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

PROVIDER: PRJNA434420 | ENA |

REPOSITORIES: ENA

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Reduced representation bisulfite sequencing (RRBS) of dairy cows and calves

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Project description:Zebrafish Primordial Germ Cells (PGCs) and somatic cells were isolated via FACS from Buc-GFP fish strain. Reduced representation bisulfite sequencing (RRBS) was performed on PGCs and somatic cells at high(6000-7000 cells per replicate), dome (7500 cells per replicate)and prim-5 stages(4500-5000 cells per replicate). Two replicates were collected for each cell type and stage.

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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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Reduced representation bisulfite sequencing of equine tissue

Project description:The aim of the project was to identify the tissue-specific DNA methylation patterns of selected horse tissues, derived from two germ layers, endodermal (liver and lung) and mesenchymal (cardiac striated muscle) origin. The comparative analysis of DNA methylation patterns of the genome fraction rich in CpG dinucleotides was investigated using Reduced Representation Bisulfite Sequencing (RRBS) technique.

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Laser Capture Microdissection-Reduced Representation Bisulfite Sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse

Project description:DNA methylation is a mechanism for long-term transcriptional regulation and is required for normal cellular differentiation. Failure to properly establish or maintain DNA methylation patterns leads to cell dysfunction and diseases such as cancer. Identifying DNA methylation signatures in complex tissues can be challenging due to inaccurate cell enrichment methods and low DNA yields. We have developed a technique called Laser Capture Microdissection-Reduced Representation Bisulfite Sequencing (LCM-RRBS) for the multiplexed interrogation of the DNA methylation status of CpG Islands and promoters. LCM-RRBS accurately and reproducibly profiles genome-wide methylation of DNA extracted from microdissected fresh frozen or formalin-fixed paraffin-embedded tissue samples. To demonstrate the utility of LCM-RRBS, we characterized changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse. Compared to adjacent normal tissue, the adrenocortical tumors showed reproducible gains and losses of DNA methylation at genes involved in cell differentiation and organ development. LCM-RRBS is a rapid, cost-effective, and sensitive technique for analyzing DNA methylation in heterogeneous tissues and will facilitate the investigation of DNA methylation in cancer and organ development. Laser capture microdissection-reduced representation bisulfite sequencing and reduced representation bisulfite sequencing on human blood leukocyte, human endometrial tumor, mouse liver tissue, and mouse normal and neoplastic adrenal tissue

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