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Series GSE210404 Query DataSets for GSE210404
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
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.
 
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).
 
Contributor(s) Ehrenhofer-Murray AE, Kaur N
Citation(s) 36169220
Submission date Aug 03, 2022
Last update date Sep 30, 2022
Contact name Ann E. Ehrenhofer-Murray
Organization name Humboldt-Universität zu Berlin
Department Institut für Biologie
Street address Philippstr. 13
City Berlin
ZIP/Postal code 10099
Country Germany
 
Platforms (1)
GPL16192 Illumina MiSeq (Schizosaccharomyces pombe)
Samples (12)
GSM6429720 AEP1 (WT) + preQ1-L1, IP, rep1 (Expt1)
GSM6429721 AEP1 (WT) + preQ1-L1, IP, rep2 (Expt1)
GSM6429722 AEP1 (WT) + preQ1-L1, IP, rep3 (Expt1)
Relations
BioProject PRJNA865659

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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
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Raw data are available in SRA
Processed data are available on Series record

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