The SEQRS protocol was conducted as described with minor modifications 4 (link). The initial library was transcribed from 1 μg of input dsDNA using the AmpliScribe T7-Flash Transcription Kit (Epicentre). The reaction was treated with RNase free DNase to remove residual DNA and purified using the GeneJET RNA Purification Kit (Fermentas). 150 ng of the purified RNA library was added to RNA binding proteins containing ~50-100 nM of fusion protein. The total volume in the binding reactions was 100 μl in SEQRS buffer containing 200 ng yeast tRNA competitor and 0.1 units of RNase inhibitor (Promega) in 8-sample strip tubes. The samples were incubated for 30 minutes at 25°C prior to capture of the protein-RNA complex. The binding reaction was aspirated and the beads were washed four times with 200 μl of ice cold SEQRS buffer. After the final wash step, the resin was resuspended in elution buffer (1 mM Tris pH 8.0) containing 10 pmoles of the reverse transcription primer. Samples were heated to 65°C for 10 minutes and then cooled on ice. A 5 μl aliquot of the sample was added to a 10μl ImProm-II reverse transcription reaction (Promega). The ssDNA product was used as a template for PCR. The efficiency of the selection process was monitored by agarose gel electrophoresis.