Noi/NOTES/2014-12-20
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scRBS experiment of single mouse neuronal nucleus (Exp #2)
- This experiment continued from the the first of experiment (Exp#1) for UCLA (Dr. Fan's group)
- I had some discussion in previous experiment. For this experiment, I will MONITOR PCR in the 1st PCR carefully to prevent over-amplification of adaptor dimers.
- In addition, I will include more control either positive control and negative control in every step to make sure that where the signal comes from. I will also include and exclude unmeth lambda DNA as well.
Sample list in brief in each step
Cell lysis
- - WT_1 to WT_16 (WT 1 nu, performed by Youjin). I re-run the number of samples to make it easy to handle and track.
- For my part I will include all controls and also in the following steps
- - T_1 to T_16 (TKO 1 nu, performed by Noi).
- - T10, T100 and T0 (TKO 10nu, 100nu and 0nu, 1 each, performed by Noi)
- - 10pg of CTT with unmeth lambda DNA (duplicates). CTT is gDNA from frozen colon tumor tissue purchased from Biochain.
- - NTC with unmeth lambda DNA (duplicate),
- All samples in this step will have 60fg of unmeth lambda DNA spike in. This allows for bisulfite conversion efficiency measurement.
DNA fragmentation with MspI
- - Include