Small RNA Sample Prep Kit FAQs

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  • Sequencing


  • Reads longer than the small RNA molecule will sequence into the adapter. For this reason, we recommend sequencing for only enough cycles to cover the small RNAs of interest, or trimming the later cycles before aligning. The sequence that would need to be trimmed from the 3' end is given here for reference.

    TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACnnnnnnATCTCGTATGCCGTCTTCTGCTTG

    This is the reverse complement of the index-specific primer sequence given in the Illumina Adapter Sequences Document, with the index sequence shown as nnnnnn.

    Many small RNA libraries do not require a PhiX control lane to generate accurate matrix and phasing estimates. This is especially true in the case of samples from organisms with balanced genomes (e.g. mammalian organisms). Libraries from organisms with unbalanced genomes, or libraries with a high proportion of reads from a single template (for example, adapter reads, or samples from a tissue that expresses a single small RNA at high levels), may require use of a control lane for matrix and phasing generation. In any case, a PhiX control lane acts as a positive control for run performance and allows error rate estimation.

    This depends on the application. For expression profiling, 1–2M mapped reads is a generally accepted range. For discovery applications, an increase to 10–20M reads may be considered.

     

    This depends on the aim of the experiment. For expression profiling projects, we do not recommend longer than 36 cycles of sequencing. The small RNA molecules are normally 15–30 bases long, and sequencing beyond this point only sequences the adapter. Eighteen cycles may be sufficient. For discovery projects, it may be worthwhile to do 40–50 cycles. This will sequence into the adapter, but the adapter sequence will be long enough to be unambiguously identified and removed even on longer small RNA molecules.