Arichard:Notebook/2013/October

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October, 2013[edit]

10/01/2013[edit]

  • Started MIDAS with Alz. neu. nuc. ID #25-00+

10/02/2013[edit]

  • Forgot to turn on temperature control. Overnight MDA ran at ~22 degC instead of 30.
    • According to NEB website, Phi29 pol processes 2280 nt/min at 30 degC, and 1490 nt/min at 15 degC.
    • Based on this, I decided to continue with the experiment.
  • Spilled the tubes after adding 75% EtOH wash after precipitation.
    • Tubes 9-12 were closed already, should not have been affected.
    • Other tubes still had visible pellets, so I just added more wash and continued.

10/03/2013[edit]

File:2013 10 03 midas alz pcr1.jpg

File:2013 10 03 midas alz pcr2.jpg

  • Chris started a new MIDAS run

10/04/2013[edit]

  • Alan asked me to pool some of my libraries. I gave them new library names afterwards:
  1. AR-Alz-28-Sep17 + AR-Alz-29-Sep17 + AR-Alz-31a-Sep17 --> AR-Alz-28,29,31-Sep30
  2. AR-Alz-31b-Sep17 --> AR-Alz-31b-Sep17 (No change, want to sequence separately)
  3. AR-Alz-30,27-Sep17 + AR-Alz-26,28a-Sep20 --> AR-Alz-26,27,28,30-Sep30
  4. AR-Alz-28,29-Sep17 + AR-Alz-25,30-Sep20 --> AR-Alz-25,28,29,30-Sep30
  5. AR-Alz-29,30-Sep20 + AR-Alz-26,28b-Sep20 --> AR-Alz-26,28,29,30-Sep30

File:2013 10 04 tagment test.jpeg

10/08/2013[edit]

  • Meeting with Professor Zhang, Jeff, and Chris to discuss issue of low mapping rates.
    • Zhang suggested that we repeat the tagmentation of chromosome samples, but include a protease condition.
  • Started a MIDAS run with 4 arrays of 25-00+, 2 arrays with SW480 (cancer line), and 2 NTC arrays.

10/09/2013[edit]

  • 2nd day of MIDAS

10/10/2013[edit]

File:2013 10 10 midas pcr1.jpeg

File:2013 10 10 midas pcr2.jpeg

10/16/2013[edit]

File:2013 10 16 qmda contamination test.jpg

10/24/2013[edit]

File:2013 10 24 pgp1chr tagment.jpg