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| Status |
Public on May 02, 2017 |
| Title |
High-throughput and site-specific identification of 2'-O methylation sites using Ribose Oxidation sequencing (RibOxi-Seq) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We report our newly developed method for high-throughput sequencing of 2'-O methylation sites using positive signal and site specific approach. The pilot experiment using MiSeq generated ~2.5 million reads per sample. The 2'-O methylation site identification produced a promising distribution pattern matching known sites. For accurate and sensitive base call, >10 million reads are required per sample as evidenced in the NextSeq experiment.
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| Overall design |
Total RNA extracted are aliquoted either as control or oxidized samples. The control RNAs are digested and subjected to custom small RNA sequencing library preparation, while the oxidized group has additional steps after digestion to oxidize RNA ends to selectively enrich fragments with 2'-O methylated terminal base for subsequent library preparation.
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| Contributor(s) |
Zhu Y, Pirnie SP, Carmichael GG |
| Citation(s) |
28495677 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 HD072418 |
Nuclear-retained long noncoding RNAs |
UNIVERSITY OF CONNECTICUT HEALTH CENTER |
Gordon G Carmichael |
|
| Submission date |
Mar 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Gordon G. Carmichael |
| E-mail(s) |
carmichael@uchc.edu
|
| Organization name |
UConn Health
|
| Department |
Genetics and Genome Sciences
|
| Street address |
263 Farmington Avenue
|
| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06030-3301 |
| Country |
USA |
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| Platforms (2) |
| GPL15520 |
Illumina MiSeq (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA380389 |
| SRA |
SRP102441 |
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