Unknown,Transcriptomics,Genomics,Proteomics

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Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing

ABSTRACT: We applied the solution hybrid selection approach to the enrichment of CpG islands (CGIs) and promoter sequences from the human genome for targeted high-throughput bisulfite sequencing. A single lane of Illumina sequences allowed accurate and quantitative analysis of 1 million CpGs in more than 21,408 CGIs and 15,946 transcriptional regulatory regions. More than 85% of capture probes successfully yielded quantitative DNA methylation information of targeted regions. In this study, we generated genome-wide, single-base resolution DNA methylation maps in three of the most commonly used breast cancer cell lines.Differentially methylated regions (DMRs) were identified in the 5?-end regulatory regions, as well as the intra- and intergenic regions, particularly in the X chromosome among the three cell lines. The single CpG resolution methylation maps of many known tumor suppressor genes were also established in the three cell lines. Here we present a novel approach that combines solution-phase hybrid selection and massively parallel bisulfite sequencing to profile DNA methylation in targeted CGI and promoter regions. We designed 51,466 single strand DNA oligonucleotides (160-mer) which target 23,441 CGIs and the transcription start sites of 19,369 known genes in the human genome. The synthetic long DNA oligonucleotides were converted into biotinylated RNA probes for solution-phase hybridization capture of target DNA. The captured genomic DNA was treated with sodium bisulfite, amplified by PCR and sequenced using Illumina GA IIx sequencer.

ORGANISM(S): Homo sapiens

SUBMITTER: Huidong Shi

PROVIDER: E-GEOD-26826 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing.

Lee Eun-Joon EJ Pei Lirong L Srivastava Gyan G Joshi Trupti T Kushwaha Garima G Choi Jeong-Hyeon JH Robertson Keith D KD Wang Xinguo X Colbourne John K JK Zhang Lu L Schroth Gary P GP Xu Dong D Zhang Kun K Shi Huidong H

Nucleic acids research 20110723 19

We applied a solution hybrid selection approach to the enrichment of CpG islands (CGIs) and promoter sequences from the human genome for targeted high-throughput bisulfite sequencing. A single lane of Illumina sequences allowed accurate and quantitative analysis of ~1 million CpGs in more than 21,408 CGIs and more than 15,946 transcriptional regulatory regions. Of the CpGs analyzed, 77-84% fell on or near capture probe sequences; 69-75% fell within CGIs. More than 85% of capture probes successfu ...[more]

PMID: 21785137

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Dataset Information

Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing

Publications

Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing.

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