White Whale - Crassostrea gigas Public Datasets

This directory contains research and documentation of public datasets with RNA-seq and DNA methylation data for Crassostrea gigas (Pacific oyster) and Magallana gigas (updated genus name).

Directory Structure

• code/ - Scripts for downloading the identified datasets (see code/HOW-TO.md)
• ncbi-datasets/ - Documentation of datasets found in NCBI databases
• literature-review/ - Information from published studies
• dataset-summaries/ - Consolidated summaries of identified datasets
• file-size-estimates/ - Estimates of cumulative file sizes for datasets

Research Scope

This research focuses on identifying publicly available datasets containing:

• RNA-seq data
• DNA methylation data (including bisulfite sequencing, MeDIP-seq, etc.)

For each dataset, we aim to collect:

• Number of samples
• Tissue types analyzed
• Environmental conditions
• Estimated cumulative file size
• Access information (SRA accessions, GEO series, etc.)

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 contains a downloader that fetches the identified DNA methylation datasets from NCBI SRA. Sequencing runs are discovered live from NCBI (no accession numbers are hardcoded), so you always get the real 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_roberts --dry-run  # preview safely
python3 download_methylation_data.py --dataset wgbs_roberts # download

New to this? Start with the step-by-step code/HOW-TO.md. For all options and troubleshooting, see code/USAGE.md.

Last Updated

• Created: December 2024
• Updated: June 2026 — added data downloader (code/)