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| Status |
Public on Sep 10, 2020 |
| Title |
DeepH&M: Simultaneous determination of single-CpG hydroxymethylation and methylation levels from enrichment and restriction enzyme sequencing methods |
| Organism |
Mus musculus |
| Experiment type |
Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Other
|
| Summary |
Increased appreciation of 5-hydroxymethylation (5hmC) as a stable epigenetic mark, which defines cell identity and disease progress, has engendered a need for cost-effective, but high-resolution 5hmC mapping technology. Current enrichment-based technologies provide cheap, but low-resolution and relative enrichment of 5hmC levels while single base-resolution methods can be prohibitively expensive to scale up to large experiments. To address this problem, we developed a deep learning-based method “DeepH&M”, which integrates enrichment and restriction enzyme sequencing methods to simultaneously estimate absolute hydroxymethylation and methylation levels at single CpG resolution. Using 7-week-old mouse cerebellum data for training DeepH&M model, we demonstrated that the 5hmC and 5mC levels predicted by DeepH&M were in high concordance with gold standard data predicted by TAB-seq and WGBS. The DeepH&M model can be applied to 7-week old frontal cortex and 79-week cerebellum revealing the robust generalizability of this method to other tissues from various biological time points.
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| |
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| Overall design |
WGBS, TAB-seq were generated for 7w and 79w mouse cerebellum and cortex. RNA-seq were generated for 7w and 79w mouse cerebellum.
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| Contributor(s) |
He Y, Wang T |
| Citation |
https://0-doi-org.brum.beds.ac.uk/10.1126/sciadv.aba0521
|
| Submission date |
Nov 08, 2019 |
| Last update date |
Sep 10, 2020 |
| Contact name |
Daofeng Li |
| E-mail(s) |
lidaof@gmail.com
|
| Phone |
(314) 286-0866
|
| Organization name |
Washington University in St. Louis
|
| Department |
Genetics
|
| Lab |
Ting Wang Lab
|
| Street address |
4515 McKinley Avenue
|
| City |
SAINT LOUIS |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
|
| Samples (24)
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| Relations |
| BioProject |
PRJNA588377 |
| SRA |
SRP229336 |
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