Are there any protocol modifications when using degraded RNA as input into library preparation?

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For whole transcriptome library preparation with FFPE samples, the RNA may be degraded enough to omit the fragmentation step and proceed directly to adapter ligation. In these cases, the FFPE-derived RNA will benefit from an additional kinase step prior to adapter ligation and an overnight ligation reaction. We recommend contacting your local Field Applications Scientist if working with degraded samples.

For small RNA library preparation, when starting from total RNA with a low RIN, the miRNA quantity could be over-estimated on the Agilent® Small RNA chip, so more input into ligation is recommended. Ideally, use >10 ng of miRNA.

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