Noi/NOTES/2014-12-20

From ZhangLabWiki
Revision as of 09:03, 14 January 2015 by >Noi (Created page with "= scRBS experiment of single mouse neuronal nucleus (Exp #2) = '''Back to calendar'''<br> * This experiment continued from the the first of exper...")
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search

scRBS experiment of single mouse neuronal nucleus (Exp #2)

Back to calendar

  • 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