Kevin H. Wong’s Open Lab Notebook

Single-cell genomics, coral biology and bioinformatics.

Kevin H. Wong

Hello! I’m Kevin H. Wong, an Assistant Scientist at the University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science. My research uses bulk and single-cell molecular approaches, genomics and bioinformatics to understand how marine invertebrates respond to climate change stressors.

This notebook is where I share my work: lab work, analyses, troubleshooting, fixes and finished workflows. I believe science is best served by transparent, reproducible work. Questions or suggestions? Email kevinhwong1@gmail.com or visit my website.

Browse the notebook Troubleshooting notes Pipelines Wet lab protocols

Pipelines

Here are my completed bioinformatic pipelines that I work on.

Wet lab protocols

Step-by-step bench protocols, each linked to the notebook entries where it was developed and used.

Citrate synthase activity (Sigma CS0720, 96-well)
Physiology assays
Astrangia poculata

Measure citrate synthase activity, a proxy for mitochondrial density, in coral host and symbiont fractions as the DTNB reaction rate at 412 nm, normalized to protein.
Coral fixation and decalcification for TEM
Imaging
Galaxea fascicularis

Fix whole coral fragments in zinc formalin, decalcify in HCl, and post-fix single polyps in glutaraldehyde for transmission electron microscopy, keeping the remaining polyps…
Coral tissue removal, homogenization and host/symbiont separation
Tissue & cell prep
Porites astreoides
Astrangia poculata

Airbrush tissue off frozen coral fragments, homogenize the slurry, aliquot it for physiology assays, and split it into host and Symbiodiniaceae fractions.
DNA/RNA co-extraction from coral tissue (Zymo Quick-DNA/RNA Miniprep Plus)
DNA/RNA extraction
Porites astreoides

Extract DNA and RNA from the same small piece of snap-frozen coral (adult fragment or larvae) using bead-beating lysis and Zymo’s paired DNA and RNA spin columns.
ITS2 amplicon PCR for Symbiodiniaceae (incl. touchdown options)
ITS2
Symbiodiniaceae
Porites astreoides

Amplify the Symbiodiniaceae ITS2 region from coral DNA for amplicon sequencing, with high-annealing and touchdown cycling options for low-symbiont (e.g. bleached) samples.
Nanopore direct RNA sequencing on the MinION
Nanopore
Transcriptomics

Workflow notes for native RNA sequencing on an Oxford Nanopore MinION (SQK-RNA002 + R9.4.1 flow cell): input requirements, library prep at a glance, flow cell loading and…
Polar metabolite extraction for LC-MS
Metabolomics
Porites astreoides
Montipora capitata

Extract polar metabolites from snap-frozen coral larvae, juveniles or adult clippings in cold methanol:acetonitrile:water with formic acid, neutralize, and load LC-MS…
S-adenosylmethionine (SAM) ELISA
Physiology assays
Astrangia poculata

Quantify S-adenosylmethionine, the methyl donor for DNA methylation, in coral host tissue by ELISA (BioVision SAM ELISA kit).
Symbiodiniaceae cell density (hemocytometer counts)
Physiology assays
Symbiodiniaceae

Count symbiont cells in coral larvae or tissue homogenates on a hemocytometer, and normalize to larva number or coral surface area.
Total antioxidant capacity (OxiSelect TAC assay)
Physiology assays
Porites astreoides

Measure copper-reducing total antioxidant capacity of coral host tissue against a uric acid standard curve (Cell Biolabs OxiSelect STA-360).
Total protein (alkaline digestion + Pierce BCA assay)
Physiology assays
Porites astreoides

Solubilize protein from coral homogenates or larvae with NaOH, neutralize, and quantify with the Pierce BCA microplate assay.
WGBS library prep (Zymo Pico Methyl-Seq)
DNA methylation
Porites astreoides

Bisulfite-convert 10 ng of coral genomic DNA and build indexed whole-genome bisulfite sequencing libraries with the Zymo Pico Methyl-Seq kit, with QC and a re-amplification…
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All wet lab protocols →

Recent notebook entries

Rebuilding the OrthoFinder environment on Pegasus with micromamba

Troubleshooting
Comparative genomics
HPC & computing
Oct 15, 2026

SATURN: preparing the human and fly immune datasets for the pLM benchmark

Analysis
scRNA-seq
Comparative genomics
HPC & computing
Oct 15, 2026

SATURN: OrthoFinder orthogroups, and how six gene groupings place species together

Analysis
Mnemiopsis leidyi
scRNA-seq
Comparative genomics
Oct 15, 2026

SATURN: what the ESMC embeddings are, how macrogenes relate to orthogroups, and a K sweep

Analysis
Mnemiopsis leidyi
scRNA-seq
Comparative genomics
Oct 9, 2026

SATURN: ESM-1b vs ESMC-600M, ortholog benchmark and macrogene composition across species

Analysis
Mnemiopsis leidyi
scRNA-seq
Comparative genomics
Oct 8, 2026

SATURN 4-species: ESM-1b vs ESMC-600M embeddings for macrogenes

Analysis
Mnemiopsis leidyi
scRNA-seq
Comparative genomics
HPC & computing
Oct 6, 2026

Pdam 31298: Cell Ranger → GeneExt → CellBender run

Analysis
Pocillopora damicornis
scRNA-seq
May 7, 2026

Obtaining sequences for HCR in Nvec

Analysis
Nematostella vectensis
scRNA-seq
Imaging
Jan 15, 2026
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All entries →

How this notebook is organized

  • Notebook: dated entries of what I did and what happened: lab work, analyses and troubleshooting.
  • Pipelines: complete computational workflows, maintained in place with a changelog.
  • Wet Lab Protocols: step-by-step bench protocols, each linked to the notebook entries that used it.
  • Projects: notebook entries grouped by research project.

The notebook links to GitHub repositories with more detail. Built with Quarto and Claude; originally built with Jekyll Now (Barry Clark) and material from many open lab notebooks. Thanks to all.

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