September 2024 goals and daily notebook entries.

Creating a functional annotation file for Acropora pulchra de novo transcriptome.

August 2024 goals and daily notebook entries.

July 2024 goals and daily notebook entries.

June 2024 goals and daily notebook entries.

May 2024 goals and daily notebook entries.

April 2024 goals and daily notebook entries.

March 2024 goals and daily notebook entries.

Code is inspired by this post, this post, and this post.

Objective:

February 2024 goals and daily notebook entries.

Comparison of deep dive Acropora pulchra E5 samples processed with PolyA to rRNA depletion heatwave gametogenesis samples

Histological image analysis for Acropora pulchra decalcified tissues

January 2024 goals and daily notebook entries.

Mapping sequences from Acropora pulchra coral samples from adult colonies exposed to marine heatwave conditions in Moorea, French Polynesia in March/April 2022 and their offspring (larvae) collected from coral spawning in October 2022 to a Acropora pulchra de novo transcriptome.

Mapping sequences from Acropora pulchra coral samples from adult colonies exposed to marine heatwave conditions in Moorea, French Polynesia in March/April 2022 and their offspring (larvae) collected from coral spawning in October 2022 to an unpublished Acropora pulchra genome.

Protocol for usage of the Thermo Scientific NanoDrop 2000c Spectrophotometer

Designing a workflow to create a de novo transcriptome for Acropora pulchra

Testing how to extract High Molecular Weight DNA for Acropora pulchra sperm

Alignment comparison of the Pocillopora effusa genome to the Pocillopora verrucosa and Pocillopora meandrina genomes for E5 molecular RNASeq data

Goal:

Use Acropora pulchra samples from Mo’orea, French Polynesia, sampled on January 15th 2022 from the north shore backreef site Mahana (17°29’13.9”S 149°53’14.7”W) to create a de novo transcriptome for A. pulchra. Extracted samples (August 23rd 2022) where concentrated using the Zymo RNA Clean and Concentrate Kit on April 25th 2023 at URI.

Alignment comparison of the Pocillopora meandrina genome to the Pocillopora verrucosa genome for E5 molecular WGBS data

Alignment comparison of the Pocillopora meandrina genome to the Pocillopora verrucosa genome for E5 molecular RNASeq data

Goal

Objective:

Whole Genome Bisulfite Sequencing (WGBS) Workflow created by Hollie M. Putnam on 20201206

Check for required software on Bluewave

Update software to latest version

• fastqc
• MultiQC
• fastp
• HiSat2
• Samtools
• StringTie
• gffcompare
• Python

This post includes the full notebook for Sept-Oct 2022 Acropora coral spawning and field expedition in Moorea, French Polynesia. These notebook posts by DM Becker-Polinski are updated in order of most recent to oldest.

Zymo Duet DNA/RNA Extraction Protocol for Gametogenesis January 2022 samples

Histology Protocol

For processing in Mo’orea

IN PROGRESS

Titrations to Track Total Alkalinity in the CBLS WetLab Tank System

Overview

Overview

Adding RNASeq and WGBS Sequence Files to NCBI Sequence Read Archive

Pocillopora spp. RNAseq QC, Alignment, Assembly Bioinformatic Pipeline

Weekly Titrations to Track Total Alkalinity in the Coral Polyp Bailout Tank System

Protocol for PocHistone Sanger Sequencing Prep for the Remaining 22 Samples

Processing Ariana’s Montipora capitata Larval Development Physiological Samples from July 2020

Protocol for PocHistone Sanger Sequencing Prep for the Remaining 28 Samples

Counting the E5 September and November 2020 Endosymbiont Samples

Processing the E5 January, March, September, and November 2020 Instantaneous Calcification Samples

Protocol for PocHistone Amplification and Test Sanger Sequencing Prep