ddRADseq size selection
As we don’t have access to a Pippin-Prep, performed size selection old school by gel excision.
- Large gel
- 150 ul TBE
- 2.25 g agarose
- 7.5 ul ethidium bromide
- Loaded each sample with ladder on both sides
- Ran gel for about 2.5 hours at 120V
- Excised three gel pieces for each sample
- 200bp: 275-300bp fragment including 76bp adapter sequence
- 300bp: 375-400bp fragment including 76bp adapter sequence
- 400bp: 475-500bp fragment including 76bp adapter sequence
- Extracted DNA using Qiagen QIAquick PCR Purification
- surprised to see a lot of DNA in some tubes. enough to make a clear mass that partially blocked column
- eluted in 10ul H2O and put in freezer
Note slight smear of digested DNA within sample lanes - confirms that there was DNA to excise.