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GeneExt

Resources

Sample information

Background

Goal

Single-cell RNAseq Analysis Central Document

DNA Methylation Sequencing Analysis Central Document

Goal: To re-analyze the 10X single cell data with the combined genomic references of Galaxea fasicularis and potential symbionts

Analyzing fresh vs frozen single cell preprations

Troubleshooing OrthoFinder to compare species orthologs

Table of Contents

Map KEGG terms to genome

Goal:

• To assess the quality of our single cell data on a control (ambient) sample

Testing the WGBS methylation calling pipeline from Epidiverse.

KOFamScan for P. astreoides

Bis-SNP analysis

This post is inspired by E. Chille’s and D. Becker’s posts on genomic functional annotations.

Thermal Stress

Documentation

Goal: to create a protocol that preserves live coral tissue for TEM imaging

Code is inspired by this post

Welcoming Galaxea fascicularis to the Cnidarian Immunity Lab!

• This post describes the onboarding process of Galaxea fascicularis to the Cnidarian Immunity lab at RSMAES.

This post is to troubleshoot coral nuclei isolations for single cell ATAC-seq. I will be troubleshooting protocols from multiple papers and on a few species.

This this my previous WGBS scripts to archive. This analysis includes all samples, which I am not currently using for my analysis anymore.

Porites bleaching TagSeq Bioinformatics

Porites astreoides Genome Annotation

Goal: To re-extract DNA from symbiont pellets to increase chances of amplifying symbiont ITS2 region DNA rather than host mitochondria.

Touchdown PCR for ITS2 processing

Goal

Goal

Goal

Goal: aligning TagSeq data to the Mansour Porites astreoides reference transcriptome

First attempt at training AUGUSTUS with BUSCO

20211021

Creating new ref folders

Goal

20210817

Goal

Project: Mcap2020

Goals

Goal

Goal

Protocol for Airbrushing tissue from coral

Project: Thermal Transplant Molecular, Holobiont Integration (ES)

Project: Thermal Transplant Molecular

Project: Thermal Transplant Molecular

Project: Thermal Transplant Molecular

Project: Thermal Transplant Molecular

Project: Thermal Transplant Molecular

Project: Thermal Transplant Molecular

Project: Thermal Transplant Molecular

Protocol For Using the Zymo Pico Methyl Seq Library Prep Kit

Project: Symbiont Integration

Project: Thermal Transplant Molecular

Project: Thermal Transplant Molecular

Project: Thermal Transplant Molecular

Project: Symbiont Integration

Project: Symbiont Integration

Project: Thermal Transplant Molecular

Project: Thermal Transplant Molecular

Project: Thermal Transplant Molecular

DNA extractions for Porites Thermal Transplant ADULTS BATCH #8

Project: Porites Bleaching 2019

Project: Porites Genome Assembly

Project: Porites Genome Assembly

Project: Porites Bleaching 2019

Project: Porites Bleaching 2019

Project: Porites Bleaching 2019

Project: Porites Bleaching 2019

Project: Porites Bleaching 2019

Project: Porites Bleaching 2019

Project: Porites Bleaching 2019

Project: Porites Bleaching 2019

Project: Porites Bleaching 2019

Project: Porites Bleaching 2019

Project: Porites Bleaching 2019

Project: Porites Bleaching 2019

Project: Porites Bleaching 2019

Project: Porites Bleaching 2019

Project: Porites Bleaching 2019

Project: Porites Bleaching 2019

Project: Porites Bleaching 2019

Project: Porites Bleaching 2019

Project: Porites Bleaching 2019

Project: Porites Bleaching 2019

DNA extractions for Porites Thermal Transplant ADULTS BATCH #7

Goal

Processing DNA/RNA extractions for Porites astreoides LARVAE: Batch #5

• Re-extracting sample replicates that had poor DNA or RNA quality from previous extractions

Goal

Processing DNA/RNA extractions for Porites astreoides LARVAE: Batch #4

DNA extractions for Porites Thermal Transplant ADULTS BATCH #6

Goal

Processing DNA/RNA extractions for Porites astreoides LARVAE: Batch #3

DNA extractions for Porites Thermal Transplant ADULTS BATCH #5

Goal

Processing DNA/RNA extractions for Porites astreoides LARVAE: Batch #2

DNA extractions for Porites Thermal Transplant ADULTS BATCH #4

Goal

To stream line the protocol for DNA/RNA extractions for Porites astreoides LARVAE

DNA extractions for Porites Thermal Transplant ADULTS BATCH #3

DNA extractions for Porites Thermal Transplant ADULTS BATCH #2

DNA/RNA extractions for Porites Thermal Transplant LARVAE BATCH #1

DNA extractions for Porites Thermal Transplant ADULTS BATCH #1

Goal

To test the protocol for DNA/RNA extractions for airbrushed homogenates, larvae, and adult fragments of Porites astreoides for the Thermal Transplant 2017/2018 experiment.

Goal

To test the protocol for DNA/RNA extractions for airbrushed homogenates of Porites astreoides for the Thermal Transplant 2017/2018 experiment.

Goal

To stream line the protocol for DNA/RNA extractions for Porites astreoides for the Thermal Transplant 2018 experiment and to test larval geoduk extractions for S. Gurr.

Goal: Metabolomic sample prep for Porites astreoides samples (adult and larvae)

DNA/RNA extractions for Porites Thermal Transplant Trial #4 - Adults and Larvae

DNA/RNA extractions for Porites Thermal Transplant Trial #3 - ADULTS

DNA/RNA extractions for Porites Thermal Transplant Trial #1 - LARVAE

DNA/RNA extractions for Porites Thermal Transplant Trial #2 - ADULTS

DNA/RNA extractions for Porites Thermal Transplant Trial #2 - ADULTS

DNA/RNA extractions for Porites Thermal Transplant Trial #1 - ADULTS

The goal of this protocol is to determine the total antioxidant capacity (TAC) in adult coral tissues from the Porites Nutition June experiment using the OxiSelect Total Antioxidant Capacity Assay kit.

The goal of this protocol is to airbrush and homogenize adult P. astreoides fragments with PBS from the Porites Nutrition June 2019 project.

This protocol is to quantify SAM (S-Adenosylmethionine) quantities in Astrangia poculata. I used the SAM ELISA KIT from BioVision. A modified version of the kit protocol was used. Only 1-96 well plate is provided with this kit, therefore only 40 samples can be measured with 8 standards and duplicates. The following table shows the 39 samples selected for this analyses (based off a range of coloration in each treatment):

Background

Background

This protocol is used to separate coral tissue slurry that is homogenized into host (coral) and symbiont (Symbiodinaceae) fractions. The samples used in this protocol were from the Astrangia poculata nutrition experiment run by K. Wong in April 2019. Corals were snap frozen, airbrushed with filtered seawater, homogenized with a glass homogenizer, aliquoted appropriately (500 μL in each tube), and frozen at -80°C. This homogenate separation will be used for citrate synthase analyses and DNA extractions

Using the Zymo Quick-DNA Mini Prep kit on adult Astrangia poculata samples from the Astrangia Nutrition Experiment.

Troubleshooting Citrate Synthase Protocol

RNA/DNA extractions for P. astreoides genome samples

Troubleshooting Zymo Quick-DNA Mini Prep kit on adult P. astreoides homogenates.

ZYMO Quick-DNA/RNA Miniprep Plus Kit Troubleshooting

This protocol is adapted to determine total protein content using the Pierce BCA Protein Assay Kit from Thermo Scientific.

This protocol is for counting Symbiodinium cells in various coral tissues. In terms of sample preparation and final counts, please be aware of what type of tissue you are using (i.e. larvae, juvenile spat, or adult tissue).

1. Start analyzing larval Symbiodinium density and total protein samples TGA 2017 experiment
2. Outline my review chapter and develop meta-analysis hypotheses
3. Edit adult respiration r code to ensure output is correct by March 01 2018

1. Finish larval Symbiodinium density and total protein quantifications for TGA 2017 experiment
2. Finish results for TGA 2017 experiment
3. Create an outline for Ch.1 (review) PhD dissertation

Lab Intro to Open Lab Notebook on GitHub