We have had some difficulty when running GBS pools on the Pippin Prep. The pools they produce are at times showing a lack of abundance. We are running this experiment to gain insight on the following questions:
Does the Blue Pippin produce more bountiful elutions than the Pippin Prep in the 300-450bp range?
Are all lanes comparable on the Pippin Prep when it comes to quality elutions?
Are lanes comparable between the Pippin Prep and Blue Pippin?
Protocol
Pull ALF_GBS_10-11 PCR A Pool and add 100uL of TE to the pool to ensure there is enough sample to run on 8 lanes. (Pippin Prep recommends bringing DNA up to 30uL using TE, so this should not interfere).
Run Pippin Prep GBS protocol* range 300-450bp with the lanes as follows:
Lane 5: Control
Lane 4: ALF_GBS R4 (Replicate 4)
Lane 3: ALF_GBS R3
Lane 2: ALF_GBS R2
Land 1: ALF_GBS R1
Program GBS protocol on Blue Pippin and run in the same structure as listed above.
Run all 8 replicates on the BioAnalyzer
Results
ALF_GBS PP vs BP Gel:
ALF_GBS PP EPG:
ALF_GBS BP EPG:
ALF_GBS PP vs BP R1 EPG:
ALF_GBS PP vs BP R2 EPG:
ALF_GBS PP vs BP R3 EPG:
ALF_GBS PP vs BP R4 EPG: