Chris:LabNotes/sci-Methyl Seq/Calendar/2017/2017-3-13
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sci-Methyl Seq Barcode 1 Design
Background
- We want to perform an initial test to determine what the ligation efficiency is for Barcode 1 adapters. This is the initial adapter containing the "duplex UMI" along with the first barcode that is intended to ligate onto MspI-digested dsDNA (refer to "Adapter 1" in experimental plan v1 <http://genome-tech.ucsd.edu/LabNotes/index.php/Chris:LabNotes/sci-Methyl_Seq/Calendar/2017/2017-3-9>)
- Today, we will want to design the Barcode 1 adapter sequence using the following structure:
5’ [Phos]CCG----------TTDD[Barcode1]---------- 3’ (Filler 1) (Filler 2)
Barcode 1 Adapter Design
- This is from the Google Doc here <https://docs.google.com/document/d/1f6fUYy26eaqqJKdxxTBFgeVucB0uOuHPdfUKYiLDF9U/edit?usp=sharing>
- From the previous experimental design, we see that Filler 1 is somewhat extraneous (there is nothing that is intended to bind to Filler 1), while Filler 2 must have a high enough Tm in order for Adapter 2 annealing later on in the protocol.
- To simplify design, we will just remove Filler 1 from teh adapter sequence for now (may want to add in later if we want to evaluate bisulfite treatment efficiency)
- Filler 2 Tm should be ~58.8C-61.4C with a length of 20bp. These parameters are based on the P5/P7 sequences that are appropriate for KAPA library amplification.
- Using Dan's script to generate primers (primergenerator.py), we generated sevarl random Filler 2 sequences we could potentially use. For the version 1 of the design, we'll be using the following Filler 2 sequence:
Sequence primerGenerator Tm OligoAnalyzer Tm Notes GTCCCTCCTACCCGGCGTTT 57.9 61.8 (58C) Only 4-base self-dimer
- We also want to choose an appropriate Barcode 1 (using a 3-letter alphabet [AGT] in order to avoid confounding results.
- Consequently, the following is the final version of the test of Adapter 1:
5’ [Phos]CGTTAG[AGGTG]GTCCCTCCTACCCGGCGTTT 3’ DD[Barcode]------Filler 2----
- We want to try making the Adapter 1 into a double stranded adapter, which may be necessary for the T4 ligation to work (need a bigger footprint than the 2-base overhang left by MspI digestion). Consequently, we want to anneal the following complementary sequence to Adapter 1:
5’ AAACGCCGGGTAGGAGGGACCACCTCTAA 3’
- Initial tests without the dsDNA adapter resulted in no ligation.