For gel purification of Small RNA-Seq libraries, we recommend performing the size selection on the lane mix using 3 % agarose gels stained with EtBr. Prepare an equimolar lane mix (calculated from the Bioanalyzer in the range from 135 – 150 bp, i.e., the miRNA fraction), load the lane mix, and run the agarose + EtBr gel in TBE for 2 hours at 80 V. Excise the desired band(s) and avoid recovering the ~120 bp linker-linker artifacts that contain no insert. For final gel extraction, any commercially available gel extraction kit can be used.
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