I had a chance to do a side-by-side comparison of Pippin Prep (PP) and agarose gels (AG) for size selection during RNA-Seq library prep and would like to share these results with the community and get some feedback.
In the picture below, I show eight RNA-Seq libraries run on a BioAnalyzer HS DNA chip. The four sharp and high peaks are from PP while the four slightly lower and broader peaks are from AG. Equal aliquots of four adapter-ligated cDNAs were used for both platforms (so it's really 4 samples, then two techniques on each sample). Noticeably, the GS libraries have a lot more non-target material both above and below the peak, although all eight have a "bump" close to the upper size marker at 10380bp. A question: which of these would make the better candidate for submission to the sequencing center? I am leaning towards the PP as there is lesser background. Any advice from folks who are routinely using Pippin Prep for RNA-Seq?
Thanks,
Shurjo
In the picture below, I show eight RNA-Seq libraries run on a BioAnalyzer HS DNA chip. The four sharp and high peaks are from PP while the four slightly lower and broader peaks are from AG. Equal aliquots of four adapter-ligated cDNAs were used for both platforms (so it's really 4 samples, then two techniques on each sample). Noticeably, the GS libraries have a lot more non-target material both above and below the peak, although all eight have a "bump" close to the upper size marker at 10380bp. A question: which of these would make the better candidate for submission to the sequencing center? I am leaning towards the PP as there is lesser background. Any advice from folks who are routinely using Pippin Prep for RNA-Seq?
Thanks,
Shurjo
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