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This dataset comprises mRNA that was extracted from Laternula elliptica developmental stages (blastula to juvenile) and sequenced (n=3 pools of 200 individual per stage). The resulting sequence data was analysed and the following results files and analysis scripts are available here: Results files from differential gene expression analysis in edgeR (edgeR_DE), results files from WGCNA analysis (WGCNA). Data collection was carried out over Hangar Cove Rothera Point, Adelaide Island, in Ryder Bay, from 2018-04-25 to 2018-09-25 by researchers with the British Antarctic Survey. The data was collected as part of research on the developmental biology of molluscs. This work was supported by UKRI Natural Environment Research Council (NERC) Core Funding to the British Antarctic Survey, a DTG Studentship (Project Reference: NE/J500173/1) and a Junior Research Fellowship to VAS from Wolfson College, University of Cambridge.