FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing.
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ABSTRACT: To accelerate previous RNA structure probing approaches, which focus on analyzing one RNA sequence at a time, we have developed FragSeq, a high-throughput RNA structure probing method that uses high-throughput RNA sequencing to identify single-stranded RNA (ssRNA) regions from fragments generated by nuclease P1, which is specific for single-stranded nucleic acids. In the accompanying study, we show that we can accurately and simultaneously map ssRNA regions in multiple non-coding RNAs with known structure in experiments probing the entire mouse nuclear transcriptome. We carried out probing in two cell types to assess reproducibility. We also identified and experimentally validated structured regions in ncRNAs never previously probed.
ORGANISM(S): Mus musculus
PROVIDER: GSE24622 | GEO | 2010/11/07
SECONDARY ACCESSION(S): PRJNA132445
REPOSITORIES: GEO
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