Monday, 10/26/15

9:30 am – 7:00 pm, 9:00 pm – 11:00 pm

Deep seq prep

  • continued with deep-seq prep
  • finished second strand synthesis
  • ran clean up on DNA-XP beads from Bauer
  • ran adaptor ligation. premixed adaptor and enzyme mix (2 min on ice), this is bad it will increase adaptor dimer.
    • we’ll quantify this on the tape-station and see how much trouble it will cause.

RNAi quantification by qPCR

  • set up QPCR plate, same organization as last time.
  • cDNA row order: 4W, 4P, 2-4W, 2-4P
  • ran tape-station (only 4 lanes left, ran ladder and lanes 1-3). looks decent.
  • ran kapa quantification

seq prep

  • previously used 1,2,4
  • setup 1 & 2 as repeats with 6,7,8 as multiplexed. (Illumina 1,2,6,7,8)
  • run new 1-5 multiplexed together (Illumina 1,2,3,4,5)
  • submit for 20 uL, 2x single lanes.
    KappaQuant_151026

References to cut (sad, I like these papers)

  • Killian 2015
  • Kharchenko 2011
  • Ernst 2011 (ENCODE)
  • Ram 2010 (ENCODE)
  • Li 2015
  • Galupa 2015, (Heard Lab)
  • Rivera 2013 (Ren Lab)
  • Gomez-Diaz (Corces lab)
  • Rosa 2014

maybe cut

  • Gorkin (Ren Lab)
  • Gibcus (Dekker Lab)
  • Bernstein & Lander 2007 (~idea founder but old)
  • Simon and Kingston 2013
  • Boyle, Yamada, and Beliveau 2012 to supplement, Chen 2015 to supplement?

notes

  • Bickmore 2013;Gibcus 2013;Levine 2014;Gorkin 2014;Sexton 2015;Galupa 2015;
  • 8-10 Bernstein 2007;Rivera 2013;Bickmore 2013;
  • Bickmore 2013;Gibcus 2013;Levine 2014;Gorkin 2014;Sexton 2015;Galupa 2015;Bickmore 2013 (1);
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