Extraction plan for actual samples
Kaitlyn ran DNA samples from protocol test 3 and test 4 on the Bioanalyzer. You can see her results in this notebook post. Based on her findings, I need to use a TissueTearor at setting 1 for 10 seconds to lyse the samples before incubation. I will also remove RNA from the DNA samples. The official protocol can be found here.
I have 10 gonad samples per pH treatment (ambient or low). Because 20 samples is a lot to work with at once, I’ll do 2 days of DNA extractions with 10 samples each. I randomly selected which ambient and low pH samples to extract in each batch. The IDs correspond to names on histology photos in this folder. Below are diagrams for each histology block:
Figures 1-5. Location of each tissue sample on histology blocks.
Batch 1: I’ll extract DNA from this batch tomorrow.
Low pH:
- 6-T1
- 9-T2
- 2-T1
- 5-T3
- 4-T3
Ambient pH:
- UK-07
- 12-T6
- UK-04
- UK-03
- UK-01
Batch 2: I’ll extract DNA from this batch on Tuesday.
Low pH:
- 1-T3
- 7-T2
- 8-T2
- 10-T3
- 3-T1
Ambient pH:
- UK-06
- 11-T4
- UK-05
- UK-08
- UK-02
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