Grace’s Notebook: DecaPod Submitted to Apple, RNA Extraction plan for Mon/Tues

Today I submitted DecaPod RSS feed to Apple for approval to be published on iTunes! I also picked out some tubes for Tri-reagent RNA extraction without lyophilizing (it’s broken again) for Monday or Tuesday next week to get things moving again.


Instructions on how to submit a podcast to iTunes from WordPress: here

Also, in the process of figuring out how to get the podcast on iTunes, I made a soundcloud account with the podcast episodes… isn’t actually necessary for publishing on iTunes… but here is the link anyway:

Tri-reagent RNA Extraction

The lyophilizer is out of commision again… Sam and I will be notified when it is usable again.

In the meantime, we’Ll try out the Tri-reagent protocol on some extra samples (an extra tube as well as some extra tubes from Day 26) without lyophilizing to see what our yield are like and if the samples are clean (Nanodrop/Bioanalyzer).

GitHub Issue #393

from Grace’s Lab Notebook

Converting space delimited to tab delimited

awk -v OFS="\t" '$1=$1' /Users/sr320/Desktop/Qiagen/Qiagen-combined.bed

Yaamini’s Notebook: Gigas Broodstock DNA Extraction Part 8

Sample extraction: Day 1

Based on Sam’s response in this issue, I was safe to extract DNA using the TissueTearor at setting 1 for 10 seconds for the following samples:

Low pH:

  • 6-T1
  • 9-T2
  • 2-T1
  • 5-T3
  • 4-T3

Ambient pH:

  • UK-07
  • 12-T6
  • UK-04
  • UK-03
  • UK-01

Kailtyn and I followed this protocol. Here are some notes:

  • Step 1: Kaitlyn carved out the tissue from histology blocks while I was in class. There are definitely some samples that I cannot re-extract DNA from or try and extract RNA from.

Table 1. Mass of samples used for DNA extractions.

Sample ID Mass (mg)
2-T1 19.7
4-T3 19.8
6-T1 20.0
5-T3 20.0
9-T2 19.6
12-T6 20.0
UK-03 19.8
UK-01 19.7
UK-04 20.0
UK-07 19.9


Figure 1. Histology blocks after carving.

  • Step 10: Kaitlyn removed sample 2-T1 from the heat block after 16 minutes of ethanol evaporation. She saw some ethanol left in the rest of the samples, so she pipetted the supernatant. The remaining samples were incubated on the heating block an additional 5 minutes (20 minutes total), then removed.
  • Step 11: UK-07 was dropped, but nothing spilled out (from what we could tell)
  • Step 12: Taught Kaitlyn how to use the TissueTearor!


Figure 2. Kaitlyn using the TissueTearor.

  • Step 17: Incubated samples with RNase an extra 5 minutes while waiting for the heat block to reach 80ºC.
  • Step 18: Relabeled some sample tubes (markings on either top or side had rubbed off) after the fourth 10 minute incubation and one minute vortex. Both labels on UK-03 rubbed off.
  • Steps 28-32: Kaitlyn needed to leave, but she wanted to learn how to use the Qubit. We decided to save this series for Friday.

I stored the samples in the fridge. We’ll see how we did tomorrow!

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from the responsible grad student