After confirming that the DNA available for this project looked good, I performed bisulfite treatment on the following gDNA samples:
- 1NF11
- 1NF15
- 1NF16
- 1NF17
- 2NF5
- 2NF6
- 2NF7
- 2NF8
- NF2_6
- NF2_18
- M2
- M3
Sample names breakdown like this:
1NF#
1 = Fidalgo Bay outplants
NF = Fidalgo Bay broodstock origination
# = Sample number
2NF#
Same as above, but:
2 = Oyster Bay outplants
NF2_# (Oysters grown in Oyster Bay; DNA provided by Katherine Silliman)
NF2 = Fidalgo Bay broodstock origination, family #2
# = Sample number
M2/M3 = C.gigas from Katie Lotterhos
Followed the guidelines of the TruSeq DNA Methylation Library Prep Guide (Illumina).
Used the EZ DNA Methylation-Gold Kit (ZymoResearch) according to the manufacturer’s protocol with the following changes/notes:
- Used 100ng DNA (per Illumina recs; Zymo recommends at least 200ng for “optimal results”).
- Thermal cycling was performed in 0.5mL thin-wall tubes in a PTC-200 (MJ Research) using a heated lid
- Centrifugations were performed at 13,000g
- Desulphonation incubation for 20mins.
DNA quantity calculations are here (Google Sheet): 20151218_oly_bisulfite_calcs
Samples were stored @ -20C. Will check samples via Bioanalyzer before proceeding to library construction.
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