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Status |
Public on Sep 30, 2022 |
Title |
Identification of queuosine-modified RNAs in S. pombe using metabolic labelling with preQ1-L1 (Q-RIP-Seq) |
Organism |
Schizosaccharomyces pombe |
Experiment type |
Other
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Summary |
In most eukaryotes and bacteria, queuosine (Q) replaces the guanosine at the wobble position of tRNAs harboring a GUN anticodon. To investigate whether other RNAs are also Q-or preQ1-modified in Schizosaccharomyces pombe, Q-RIP-Seq was established and applied to RNAs from WT (AEP1) and qtr2∆ cells (AEP288). Metabolic labeling of RNAs with azido-propyl-preQ1 (preQ1-L1), chemical clicking of a biotin-alkyne followed by immunoprecipitation on streptavidin beads and sequencing of enriched RNAs in WT compared to qtr2∆ allowed identification of Q-modified RNAs.
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Overall design |
S. pombe cells were metabolically labelled with azido-propyl-preQ1 (preQ1-L1) to label Q-modified RNAs. RNA was extracted, chemically clocked with biotin-alkyne; labeled RNAs were enriched on streptavidin beads and subjected to HTS. HTS reads were analyzed for RNAs enriched in wt compared to qtr2∆ cells (n = 3).
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Contributor(s) |
Ehrenhofer-Murray AE, Kaur N |
Citation(s) |
36169220 |
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Submission date |
Aug 03, 2022 |
Last update date |
Sep 30, 2022 |
Contact name |
Ann E. Ehrenhofer-Murray |
Organization name |
Humboldt-Universität zu Berlin
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Department |
Institut für Biologie
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Street address |
Philippstr. 13
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City |
Berlin |
ZIP/Postal code |
10099 |
Country |
Germany |
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Platforms (1) |
GPL16192 |
Illumina MiSeq (Schizosaccharomyces pombe) |
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Samples (12)
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GSM6429723 |
AEP288 (qtr2∆) + preQ1-L1, IP-control, rep1 (Expt1) |
GSM6429724 |
AEP288 (qtr2∆) + preQ1-L1, IP-control, rep2 (Expt1) |
GSM6429725 |
AEP288 (qtr2∆) + preQ1-L1, IP-control, rep3 (Expt1) |
GSM6429726 |
AEP1 (WT) + preQ1-L1, small RNAs, - rRNA, IP, rep1 (Expt2) |
GSM6429727 |
AEP1 (WT) + preQ1-L1, small RNAs, - rRNA, IP, rep2 (Expt2) |
GSM6429728 |
AEP1 (WT) + preQ1-L1, small RNAs, - rRNA, IP, rep3 (Expt2) |
GSM6429729 |
AEP288 (qtr2∆) + preQ1-L1, small RNAs, - rRNA, IP-control, rep1 (Expt2) |
GSM6429730 |
AEP288 (qtr2∆) + preQ1-L1, small RNAs, - rRNA, IP-control, rep2 (Expt2) |
GSM6429731 |
AEP288 (qtr2∆) + preQ1-L1, small RNAs, - rRNA, IP-control, rep3 (Expt2) |
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Relations |
BioProject |
PRJNA865659 |
Supplementary file |
Size |
Download |
File type/resource |
GSE210404_Q-RIP-Seq_exp1.txt.gz |
2.6 Kb |
(ftp)(http) |
TXT |
GSE210404_Q-RIP-Seq_exp2.txt.gz |
1.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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