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| Status |
Public on Nov 24, 2020 |
| Title |
RiboMeth-seq data from Pyrococcus furiosus |
| Organism |
Pyrococcus furiosus |
| Experiment type |
Other
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| Summary |
Semiconductor sequencing of alkaline degraded total RNA from Pyrococcus furiosus annotated for ”The 23S ribosomal RNA from Pyrococcus furiosus is circularly permuted” published in Frontiers in Microbiology”
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| Overall design |
P. furiosus RNA was degraded at denaturing conditions into small fragments, long enough to be mapped by sequence alignment to the reference genome (20-40 nucleotides). The fragments were ligated to RNA oligos using a tRNA ligase that was mutated to remove its kinase activity, reverse transcribed and the cDNA used as input for Ion semiconductor sequencing. The first and last nucleotides of the inserts were recorded using the full sequence for mapping and the read-ends plotted against the sequence. 2'-O-Methylated RNA positions are protected from cleavage, and read ends from such positions are therefore underrepresented compared to the surrounding positions.
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| Contributor(s) |
Birkedal U, Nielsen H |
| Citation(s) |
33362734 |
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https://www.frontiersin.org/articles/10.3389/fmicb.2020.582022/abstract
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| Submission date |
Jun 29, 2020 |
| Last update date |
Jan 04, 2021 |
| Contact name |
Nicolai Krogh |
| E-mail(s) |
nicolaikj@sund.ku.dk
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| Organization name |
University of Copenhagen
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| Department |
Department of Cellular and Molecular Medicine
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| Lab |
RNA Group - Prof. Henrik Nielsen
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| Street address |
Blegdamsvej 3B
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| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
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| Platforms (1) |
| GPL28793 |
Ion Torrent Proton (Pyrococcus furiosus) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA642860 |
| SRA |
SRP269233 |
