|
| Status |
Public on May 12, 2022 |
| Title |
Simultaneous Detection of DNA Adenine and Cytosine Methylation using NT-seq [series1: no enrichment] |
| Organisms |
Helicobacter pylori; Escherichia coli; mixed culture metagenome |
| Experiment type |
Methylation profiling by high throughput sequencing
Other
|
| Summary |
DNA methylation plays important roles in foreign DNA defense, mismatch repair, and gene regulation in prokaryotic genomes. Existing methods for DNA methylation detection using next-generation sequencing (NGS) are incapable of simultaneously detecting multiple types of DNA methylation. Here, we present nitrite treatment followed by sequencing (NT-seq), a sequencing method to simultaneously detect adenine and cytosine methylation. We demonstrated that NT-seq reliably detects three types of methylation motifs in E. coli and H. pylori genomes. We further applied NT-seq to a microbial community standard for de novo methylation motif discovery. Finally, by coupling methyl DNA immunoprecipitation and NT-seq (DIP-NT-seq), we showed that 6mA could be accurately mapped at single-base resolution in the bacterial and eukaryotic genomes. NT-seq thus provides a simple and reliable solution for detecting multiple types of DNA methylations.
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| |
|
| Overall design |
NT-seq in both native and amplified genomic DNA without any enrichment
|
| |
|
| Contributor(s) |
Li X, Wu TP |
| Citation(s) |
35637459 |
| |
| Submission date |
Sep 17, 2021 |
| Last update date |
Jun 02, 2022 |
| Contact name |
Tao P. Wu |
| E-mail(s) |
tao.wu@bcm.edu
|
| Phone |
713-798-2805
|
| Organization name |
Baylor College of Medicine
|
| Department |
Molecular and Human Genetics
|
| Lab |
Tao Wu Lab
|
| Street address |
One Baylor Plaza, MS BCM225
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
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| Platforms (3) |
| GPL21222 |
Illumina NextSeq 500 (Escherichia coli) |
| GPL30644 |
Illumina NextSeq 500 (Helicobacter pylori) |
| GPL30645 |
Illumina NextSeq 500 (mixed culture metagenome) |
|
| Samples (14)
|
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| This SubSeries is part of SuperSeries: |
| GSE184374 |
Simultaneous Detection of DNA Adenine and Cytosine Methylation using NT-seq |
|
| Relations |
| BioProject |
PRJNA764234 |
| SRA |
SRP337636 |
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