Hello. Has anyone had a problem where, after a cDNA library preparation that includes multiple displacement amplification, runs on a GS Junior can not generate reads with greater length than around 100bp? Results from the Bioanalyzer clearly show the library to be in good shape with average read length around the 600 bp mark.The dots filter is trimming at very high percentages.Subsequent runs on libraries with no whole genome amplification using the same sequencer are very good. Might there be something in the chemistry of the MDA step that leads to incompatability with a GS Junior? Thanks.
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Hi Daniel,
The MDA amplification leads to branched DNA formation (there's mention of it here http://www.plosone.org/article/info:...l.pone.0003042 and in the subsequent reference trail) and S1 nuclease treatment is recommended to resolve this. That might be an issue in your case? -
Thanks Palecomic - I'll look into thisComment
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