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

• 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)

Last Updated

Created: December 2024