|
| Status |
Public on Jan 05, 2021 |
| Title |
Native single molecule sequencing and de novo assembly of Hepatitis B Virus to detect 5mCpG |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
Methylation of Hepatitis B Virus (HBV) DNA in a CpG context (5mCpG) can alter the expression patterns of viral genes related to infection and cellular transformation. Moreover, it may also provide clues to why certain infections are cleared, or persist with or without progression to cancer. The detection of 5mCpG often requires techniques that damage DNA or introduce bias through a myriad of limitations. Therefore, we developed a method for the detection of 5mCpG on the HBV genome that does not rely on bisulfite conversion or PCR. Moreover, using the developed technique, we have provided the first de novo assembly of native HBV DNA, as well as the first landscape of 5mCpG from native HBV sequences
|
| |
|
| Overall design |
PHH were isolated from halthy liver tissue and plated before HBV infection with different genotypes. Also investigated fine needle biopsys for HBV DNA.
|
| |
|
| Contributor(s) |
Goldsmith C, Hernandez-Vargas H |
| Citation(s) |
34003741 |
| |
| Submission date |
Dec 02, 2020 |
| Last update date |
Jun 24, 2021 |
| Contact name |
Chloe Desiree Goldsmith |
| E-mail(s) |
chloe.goldsmith@lyon.unicancer.fr
|
| Phone |
0769602496
|
| Organization name |
INSERM
|
| Department |
Cancer Research Center of Lyon
|
| Lab |
Tumor invasion and immunity
|
| Street address |
28 Rue Laennec
|
| City |
Lyon Cedex 08 |
| ZIP/Postal code |
69373 |
| Country |
France |
| |
|
| Platforms (1) |
|
| Samples (6)
|
| GSM4953612 |
HBV amplified by nested PCR, fully unmethylated control |
| GSM4953613 |
Amplified HBV methylated with M.Ssssl methyltransferase, fully methylated control |
| GSM4953614 |
HBV GA enriched form infected PHH |
|
| Relations |
| BioProject |
PRJNA682138 |
| SRA |
SRP295521 |
Less...
More...