17 January 2014

knitcitations, pander, and pandoc

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Wednesday notes



continuing work on analysis…


Test extractions to see if I can figure out problems…

  1. Compare extractions with 1 and 3 ants to see if input issue
  2. Compare RNAzol, Qiagen, and RNAzol + Qiagen
  • the Qiagen only extractions with just 1 ant each

Set up 3 reps of each using ants from Andrew’s colonies in lab

For RNAzol, followed standard protocol. Took aliquots from 102 ul elution for Nanodrop and Bioanalyzer quantification, then proceed with Qiagen RNeasy with all samples.

For Qiagen only, homogenized ant with zirconium silicate beads in 350 ul Buffer RLT. Centrifuged. Transferred supernatant to new tube, added 350 ul 70% EtOH.

  • followed Qiagen protocol using 10ul DNase only
  • stupid mistake and eluted in 170 instead of 17 ul H2O. Nanodrop results all nil
    • repeated column extraction, precipitating in 17 ul as normal
    • one sample had good yield (18 ng/ul) and quality (2.1 260/280). others were low. need to repeat to determine how much is due to double-column precipitation

Sent samples for Bioanalyzer analysis:

  1. RQ3-1R
  2. RQ1-1R
  3. RQ3-2R
  4. RQ1-2R
  5. RQ3-3R
  6. RQ1-3R
  7. RQ3-1Q
  8. RQ3-3Q
  9. Q1-1

where the first six samples were the RNAzol extractions, and the last three were the best (double) RNeasy extractions.


  • Van Houten lab meeting - using R
  • Ecolunch
  • Gotelli lab meeting - markdown



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