This electronic notebook provides the scripts employed to analyze gene expression dynamics across developmental stages (planulae and adults) of the coral Porites astreoides inhabiting shallow (10 m) and mesophotic (45 m) reefs in Bermuda. All the scripts employed for the analysis can be found in the project electronic notebook.

This protocol details the steps and code used to detect and quantify ribosomal RNA in Illumina sequencing reads. Coral RNA samples were sequenced using an Illumina Stranded mRNA workflow (polyA enrichment).

This protocol details the step-by-step use of the PreSens/Loligo Microplate respiration system for measuring respiration and photosynthesis of coral planulae.

This protocol details the step-by-step programming use of the Apex Fusion system for pH-temperature experiments performed at the Hawaiian Institute of Marine Biology (HIMB) in June-July 2022 with planulae of the coral species Montipora capitata and Pocillopora acuta.
All the equipment used belongs to the Putnam Lab.

Pipeline for processing and reconstruction of X-ray tomography data of coral recruits’ skeleton, acquired with synchrotron radiation at (BAMline), the imaging beamline at BESSY (HZB - Helmholtz-Zentrum Berlin, Germany). Data preprocessing and reconstruction were performed using the in-house Octave-based reconstruction pipeline in the lab of Dr. Paul Zaslansky at Charité, Universitätsmedizin Berlin.

This post contains the bioinformatic pipeline used for analyzing Stylophora pistillata mRNA sequences, to reveal gene expression dynamics across shallow (5 m) and mesophotic (45 m) reefs under ambient (8.2 pH), intermediate-low (7.8 pH), and low (7.6 pH) pH conditions. All the scripts employed for the analysis can be found in the project electronic notebook.

Measuring 3D thickness of the skeletal septa of Stylophora pistillata primary polyps. A laboratory micro-CT (Skyscan1172, Bruker micro-CT, Belgium) was used to image the primary polyps. Scan data were viewed in 3D using CTvox (v 3.0, Brucker-microCT, Belgium) and analyzed as a stack.

Using the Hive shell for genomic analyses. Hive is a high performance computing system of the Faculty of Natural Sciences at University of Haifa. This document is intended to provide helpful commands for the Hive shell.

Using the Zymo Pico Methyl Seq Kit on the MBD enriched Stylophora shallow and mesophotic samples from the pH experiment. For this library prep I also used the E. coli Non-Methylated Genomic DNA which is not supplied with the Zymo Methyl kit.

Design of primers for Symbiodinium microadriaticum and Cladocopium goreaui to test the effect of ocean acidification on the algal endosymbiont. Samples are coming from the pH experiment with adults S. pistillata corals from shallow and mesophotic reefs.

Samples for DNA methylation are from the pH experiment with shallow and mesophotic Stylophora pistillata adults. The DNA was extracted by me with the Zymo Quick-DNA/RNA Miniprep Plus Kit, following the protocol of emmastrand.

In this Extraction I used: Wizard Genomic DNA Purification Kit, and my Protocol.

In this Extraction I used: Invitrogen RNA micro kit, my Protocol, and the company manual from page 19.

Using the Zymo Quick-DNA/RNA Miniprep Plus Kit on Stylophora pistillata shallow and mesophotic samples from the pH experiment.

In this Extraction I used: Invitrogen RNA mini kit, my Protocol, and the company manual from page 27.

These instructions allow to quantitatively assess coral physiological parameters, i.e. tissue biomass (protein concentration), algal density and chlorophyll concentration.

Follow the instructions of the Quick guide for microplate respirometry system

These instructions cover two ways to get algal cell counts using Fiji, one manual and one automated. A fluorescence microscope (Nikon Eclipse Ti, Japan) was used to image symbiotic algae (isolated from coral tissue) both in brightfield and in fluorescent light using 440 nm emission, to identify chlorophyll and to ensure counting of symbiont cells only.