White Whale - Crassostrea gigas Public Datasets

This repository documents public RNA-seq and DNA methylation datasets for Crassostrea gigas (Pacific oyster) and Magallana gigas (updated genus name), and includes a downloader for the curated methylation BioProjects.

At a Glance

	Value
Verified methylation runs	~536 (across 10 BioProjects)
Verified methylation volume	~2.6–3.0 TB
Downloadable methylation datasets	8 verified sets
RNA-seq accessions	Pending verification

See dataset-summaries/consolidated-summary.md for the full catalog.

Directory Structure

• action-plan.md — Systematic search and cataloging plan
• code/ — Scripts for downloading identified methylation datasets (HOW-TO.md)
• ncbi-datasets/ — Datasets found in NCBI (SRA, GEO, BioProject)
• literature-review/ — Key publications with associated data
• dataset-summaries/ — Consolidated inventory and metrics
• file-size-estimates/ — Size estimation methodology

Research Scope

Focus: publicly available datasets with:

• RNA-seq / transcriptome data
• DNA methylation data (WGBS, RRBS, MeDIP-seq, targeted bisulfite, etc.)

For each dataset, the documentation aims to capture sample counts, tissue types, environmental conditions, estimated file size, and access information (SRA, GEO, BioProject).

Search Terms Used

Species Names

• Crassostrea gigas
• Magallana gigas (updated genus classification)

Data Types

• RNA-seq / Transcriptome
• Bisulfite sequencing / DNA methylation
• MeDIP-seq
• WGBS (Whole Genome Bisulfite Sequencing)
• RRBS (Reduced Representation Bisulfite Sequencing)

Downloading Data

The code/ directory downloads DNA methylation datasets from NCBI SRA. Sequencing runs are discovered live from NCBI (no accessions hardcoded) and each run is validated as a Crassostrea/Magallana gigas bisulfite/MeDIP run before download, so you only ever get on-target files.

cd code
./install_dependencies.sh                                       # one-time: install SRA Toolkit
python3 download_methylation_data.py --list                     # see available datasets
python3 download_methylation_data.py --dataset wgbs_ph_ploidy --dry-run  # preview safely
python3 download_methylation_data.py --dataset wgbs_ph_ploidy   # download

Dataset IDs: wgbs_poms_adaptation, emseq_poms_gestinov, wgbs_aging_decicomp, wgbs_pesto, wgbs_transgen_infection, wgbs_ph_ploidy, medip_development, wgbs_epigenomics_series

Start with the step-by-step code/HOW-TO.md. For options and troubleshooting, see code/USAGE.md.

Last Updated

• Created: December 2024
• Updated: August 2026 — methylation catalog rebuilt from verified NCBI SRA queries; downloader now validates organism/assay per run