---
title: "Tissue subsampling for WGBS (cont.)"
author: "Kathleen Durkin"
date: "2024-04-29"
categories: ["pacifc-cod"]
format:
  html
---

We're planning on sending out samples for whole genome bisulfite sequencing (WGBS) to examine methlation in our cod samples. Today I finished compiling the blood and gill tissue and prepped for shipping tomorrow. (See previous post on [subsampling the liver tissue samples](./2024_04_25_methylation_subsampling.qmd))

[Sample list](https://docs.google.com/spreadsheets/d/19CqqS3wOhmG7drw163v7evUylRWwOjBOdvuR-y0RqF0/edit#gid=155247170)

### Sample selection

All samples selected for methylation work are a subset of samples that were RNA sequenced. In sample selection we took consideration of RNA extraction and sequence quality, tank, genetic variability, size, and ZP3 gene haplotype.

40 total samples

-   32 liver (8/treatment)

-   4 blood (2 from 0\*C, 2 from 16\*C)

-   4 gill (2 from 0\*C, 2 from 16\*C)

### Subsampling protocol

Sterilized all tools in 10% bleach, then rinsed in DI water before use. Sterilized between every use.

Tissue quantity recommended by Azenta for DNA extraction from whole tissue is 10-30mg. For blood samples we just send the full blood volume. For gill tissues, which have already been subsampled for RNAseq work, all of the samples had \<10mg of tissue left so the entire remaining tissue was sampled for WGBS. This means that, for both the blood and gill samples, no tissue remained after subsampling for WGBS.

All samples were stored in a box labelled "P.cod samples for methylation" with the date (04/25/2024) and my initials (KMD) in the middle -80 freezer in FTR.

### WGBS Samples

|                  |                   |
|------------------|-------------------|
| **0C treatment** | **16C treatment** |
| 50 B             | 12 B              |
| 59 B             | 18 B              |
| 50 G             | 12 G              |
| 59 G             | 18 G              |

![Final set of liver, blood, and gill samples prepped to send for WGBS](images/IMG_8692.jpg)
