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| Status |
Public on Aug 14, 2019 |
| Title |
DNA Analysis by Restriction Enzyme (DARE) enables concurrent genomic and epigenomic characterization of single cells |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
Genome-wide profiling of copy number alterations and DNA methylation in single cells could enable detailed investigation into the genomic and epigenomic heterogeneity of tumor populations. However, current methods to do this require complex sample processing and cleanup steps, lack consistency, or are biased in their genomic representation. Here, we describe a novel single-tube enzymatic method, DNA Analysis by Restriction Enzyme (DARE), to perform deterministic whole genome amplification while preserving DNA methylation information. This method was evaluated on low amounts of DNA and single cells, and provides accurate copy number aberration calling and representative DNA methylation measurement across the whole genome. Single cell DARE is an attractive and scalable approach for concurrent genomic and epigenomic characterization of cells in a heterogeneous population.
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| |
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| Overall design |
Analysis of HepG2 and K562 copy number aberrations and methylation status in bulk genomic DNA and single cells. ESC bulk genomic DNA was used to verify the copy number aberration analysis.
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| |
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| Contributor(s) |
Cheow LF, Viswanathan R, Cheruba E |
| Citation(s) |
31418018 |
| Submission date |
Mar 19, 2019 |
| Last update date |
Nov 12, 2019 |
| Contact name |
Lih Feng Cheow |
| E-mail(s) |
lihfeng.cheow@nus.edu.sg
|
| Organization name |
National University of Singapore
|
| Department |
Biomedical Engineering
|
| Lab |
Technology Innovations for Systems Biology
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| Street address |
4 Engineering Drive 3
|
| City |
Singapore |
| ZIP/Postal code |
117583 |
| Country |
Singapore |
| |
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| Platforms (2) |
| GPL15520 |
Illumina MiSeq (Homo sapiens) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (29)
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| Relations |
| BioProject |
PRJNA528100 |
| SRA |
SRP188880 |
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