Closer to having some pooled libraries!

Sam extracted RNA using the Quick DNA/RNA Microprep Plus Kit (ZymoResearch) (post). I don’t think there is currently enough RNA in the libraries to reach the requiremets for NWGC… details in post.

Today I quickly joined his qubit result file with the hemolymph sampling data (hemo_table.csv) in R.

The resulting file: hemo_qub-for-libs.csv

The goal is to have 12 libraries accounting for each infection status and temperature treatment. Each pooled library needs to have at least 1000 ng of RNA in a sample of ~50ul. (GitHub Issue #184)

Pooled libraries to create:

Library Number Sample Day Infection status Temp trtmnt
1 9 0 NA
2 9 1 NA
3 12 0 Amb
4 12 1 Amb
5 12 0 Cold
6 12 1 Cold
7 12 0 Warm
8 12 1 Warm
9 26 0 Amb
10 26 1 Amb
11 26 0 Cold
12 26 1 Cold

*Note: the temperature treatments didn’t start until after the Day 9 sampling day.

As of now, I don’t think the pooled samples would have enough RNA to meet the requirements… for example, the samples that fall under Library 1 add up to 79.9 ng/ul.

I may need to check this again when I’m not sick.

Written on May 9, 2019