|
| Status |
Public on Sep 07, 2015 |
| Title |
Bisulfite-free and Base-resolution Analysis of 5-formylcytosine at Whole-genome Scale |
| Organism |
Mus musculus |
| Experiment type |
Methylation profiling by high throughput sequencing
Other
|
| Summary |
Active DNA demethylation in mammals involves TET-mediated oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxycytosine (5caC). However, genome-wide detection of 5fC at single-base resolution remains challenging. Here we present a bisulfite-free method for the whole-genome analysis of 5fC, based on a selective chemical labeling of 5fC and subsequent C-to-T transition during PCR. Base-resolution 5fC maps reveal limited overlap with 5hmC, with 5fC-marked regions more active than 5hmC-marked ones.
|
| |
|
| Overall design |
Utilization of cyclization-enabled C-to-T transition of 5fC (hence “fC-CET”) to obtain genome-wide map of 5fC at single-base resolution
WT and TdgKO mES cell lines. Two non-enriched input DNAs (Input: preAI), two AI labeled samples (Input: AI), two pull-down output samples.
|
| |
|
| Contributor(s) |
Xia B, Han D, Lu X, He C, Yi C |
| Citation(s) |
26344045 |
| Submission date |
Feb 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Dali Han |
| E-mail(s) |
handali294@gmail.com
|
| Organization name |
University of Chicago
|
| Department |
Department of Chemisty
|
| Street address |
5801 South Ellis Avenue
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
|
| Samples (12)
|
|
| Relations |
| BioProject |
PRJNA275968 |
| SRA |
SRP055375 |
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