Data from: Gene expression correlated with delay in shell formation in larval Pacific oysters (Crassostrea gigas) exposed to experimental ocean acidification provides insights into shell formation mechanisms ...

• Main Authors: De Wit, Pierre, Durland, Evan, Ventura, Alexander, Langdon, Chris J.
• Format: Dataset
• Language: English
• Published: Dryad 2019
• Subjects: Aragonite; Larvae; Calcification; Crassostrea gigas; Ocean acidification
• Online Access: https://dx.doi.org/10.5061/dryad.8m5v4; https://datadryad.org/stash/dataset/doi:10.5061/dryad.8m5v4

Despite recent work to characterize gene expression changes associated with larval development in oysters, the mechanism by which the larval shell is first formed is still largely unknown. In Crassostrea gigas, this shell forms within the first 24 hours post fertilization, and it has been demonstrated that changes in water chemistry can cause delays in shell formation, shell deformations and higher mortality rates. In this study, we use the delay in shell formation associated with exposure to pCO2-acidified seawater to identify genes correlated with initial shell deposition. By fitting linear models to gene expression data in ambient and low aragonite saturation treatments, we are able to isolate 37 annotated genes correlated with initial larval shell formation, which can be categorized into 1) ion transporters, 2) shell matrix proteins and 3) protease inhibitors. Clustering of the gene expression data into co-expression networks further supports the result of the linear models, and also implies an important ... : Experiment 1 (NET3) Raw read counts (with duplicates)Experiment 1 (NET3) Raw read counts (with duplicates), mapped to the oyster genome v9 coding regions.NET3_Counts_with_dups.txtExperiment 2 (NET1) Raw read counts (with duplicates)Experiment 2 (NET1) Raw read counts (with duplicates), mapped against the oyster genome v9 coding regions.NET1_Counts_with_dups.txtExperiment 1 (NET3) Raw read counts (duplicates removed)Experiment 1 (NET3) Raw read counts (duplicates removed), mapped against the oyster genome v9 coding regionsNET3_Counts_dedup.txtExperiment 2 (NET1) Raw read counts (duplicates removed)Experiment 2 (NET1) Raw read counts (duplicates removed), mapped against the oyster genome v9 coding regionsNET1_Counts_dedup.txtSupporting information - ErmineJ Functional enrichment results fileSupporting information - ErmineJ Functional enrichment results fileSI_TableS2_ERMINEJ GSR runs.project ...