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| Status |
Public on Aug 01, 2011 |
| Title |
Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
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.
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| Overall design |
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.
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| |
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| Contributor(s) |
Shi H |
| Citation(s) |
21785137 |
| |
| Submission date |
Jan 24, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Huidong Shi |
| E-mail(s) |
hshi@augusta.edu
|
| Phone |
706-721-6000
|
| Organization name |
Augusta University
|
| Department |
Georgia Cancer Center
|
| Lab |
2125 K
|
| Street address |
1120 15th Street, CN2138
|
| City |
Augusta |
| State/province |
GA |
| ZIP/Postal code |
30912 |
| Country |
USA |
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| Platforms (1) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
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| Samples (8)
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| Relations |
| SRA |
SRP005473 |
| BioProject |
PRJNA136031 |
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