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qMAP decodes RNA fragmentation dynamics

GSE330870 Mus musculus Expression profiling by high throughput sequencing 6 samples Submitted 2026/05/13 Platform GPL34328
Summary
Recent advances in small RNA research reveal that noncanonical small RNAs, such as tRNA-derived small RNAs (tsRNAs) and rRNA-derived small RNAs (rsRNAs), are more abundant than well-known microRNAs in various tissue/cell types. Distinct fragmentation of parental RNAs (e.g., tRNA and rRNA) can generate functionally diverse small RNAs. Therefore, we propose a computational tool (qMAP) to identify differential fragmentation of parental RNAs between different biological conditions. Using qMAP, we tested aging-associated differential RNA fragmentation in mouse sperm heads between young and old mice. 28S rRNA was found to exhibit the most significant differential fragmentation. One short rsRNA candidate (17-nt) and one long rsRNA candidate (44-nt) were selected as their involvement of the observed differential fragmentation of 28S rRNA. These two candidate rsRNAs were transfected into mouse embryonic stem cells (mESCs), respectively. mRNA sequencing on these mESCs revealed a distinct transcriptomic response to the 17-nt and 44-nt rsRNAs.
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Direct links to NCBI, no account and no request form: the whole study as GSE330870_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 6 samples. Raw sequencing reads are also available from ENA.

Also filed as BioProject PRJNA1465826 and SRA study SRP700231. Searching any of these in the dataset finder brings you back here.

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