Pico E5 Deepdive Checks

layout: post title: Pico Methyl-Seq library prep checks date: ‘2024-10-16’ categories: tags: [DNA, Library prep, Protocols, WGBS] projects: e5 —

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ITS2 clean-up

This post details information on ITS2 clean-up for the my ambient Mcap developmental timeseries samples from 2023 and for the POC spawning experimental samples from 2023. Mcap 2023 github repo is here and POC github is here. See Ariana’s post about the ITS2 protocol for this project.

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ITS2

ITS2 for Mcap developmental timeseries Hawaii 2023 and POC spawning 2023 sample

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ITS2

ITS2 for Mcap developmental timeseries Hawaii 2023 and POC spawning 2023 sample

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ITS2

ITS2 for Mcap developmental timeseries Hawaii 2023 and POC spawning 2023 sample

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Mcap Ribofree expression test

I am deciding what kind of depth/coverage I will need for sequencing if I proceed with the Zymo Ribofree library prep kit. I am using the gene count matrices generated through the Express Compare project. In this post, I looked at all of the Mcap Ribofree gene count matrices that I could find to assess how many genes were retained before and after filtering. I did a two-step filtering process - first, I removed all rows whose sum was zero (ie those genes were not expressed at all). Then I applied the pOverA(0.75,5).

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RNA QC

I have been having some discrepancies in my RNA QC data for AH’s sample. I have been getting “Sample too low” for a lot of samples on the Qubit, but when I run the same samples on the Tapestation, I get pretty solid concentrations. I wanted to compare data from past extractions that have done both Qubit and Tapestation. Erin Chille did RNA extractions for an Mcap 2018 larval experiment and a Ahya 2018 gamete experiment where she did Qubit and Tapestation QC on the samples. I compared those results in the figures and tables below.

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Bermuda 2023 daily notebook posts

This post includes the full notebook for the July-August 2023 Diploria labyrinthiformis coral spawning and field expedition in Bermuda at the Bermuda Institute of Ocean Sciences. My project will focus on development of D. labyrinthiformis larvae through their use of energetic stores and expression of coding and non-coding transcripts. The ENCORE team (Dr. Hollie Putnam (URI), Dr. Gretchen Goodbody-Gringley (CCMI), Dr. Sam de Putron (BIOS), Dr. Yvonne Sawall (BIOS), Dr. Brett Jameson (BIOS), Dr. Chloe Carbonne (BIOS, Flo Fields (URI), and Hailey Davis (CCMI)) are also here doing a variety of experiments with D. labyrinthiformis and Porites astreoides. Githubs for the ENCORE projects are here. Github for the developmental timeseries is here.

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Hawaii 2023 daily notebook posts

This post includes the full notebook for the June-July 2023 Montipora capitata coral spawning and field expedition in Hawaii at the Hawaii Institute of Marine Biology. My project will focus on development of M capitata larvae through their use of energetic stores and expression of coding and non-coding transcripts. Dr. Ariana Huffmyer is also conducting experiments on M. capitata larvae; her experiments are detailed in her Github notebook here. Github for the developmental timeseries is here.

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Autoclave Use

The first floor autoclave in CBLS is in room 178. It is usually unlocked, but may require swipe access.

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Spawning

Goals: create spawning and fertilization protocol for Astrangia 2021

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