Gene expression analysis of Pacific oysters (Crassostrea gigas) subjected to accute heat stress
Gene expression changes, in response to heat shock, were compared between the pre- and post-heat shocked oysters. The RNA-seq analysis was performed using the Tuxedo suite. The Tuxedo suite was used to align the raw sequencing reads to the published Crassostrea gigas genome (ENSEMBL 1.24), quantify,...
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| Format: | Dataset |
| Language: | unknown |
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figshare
2015
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| Online Access: | https://dx.doi.org/10.6084/m9.figshare.1344541.v1 https://figshare.com/articles/dataset/Gene_expression_analysis_of_Pacific_oysters_Crassostrea_gigas_subjected_to_accute_heat_stress/1344541/1 |
| Summary: | Gene expression changes, in response to heat shock, were compared between the pre- and post-heat shocked oysters. The RNA-seq analysis was performed using the Tuxedo suite. The Tuxedo suite was used to align the raw sequencing reads to the published Crassostrea gigas genome (ENSEMBL 1.24), quantify, and calculate differential gene expression between the two sample groups. This project for the Univ. of Washington class, FISH546 Winter 2015, contains the data products generated during the analysis, as well the Jupyter (IPython) notebook used for the analysis. The Jupyter notebook is included to encourage reproducibility and can be used to re-run the analysis in a semi-autonomous fashion. README.md Products/: This directory contains all products generated from the analysis of this project. The products within are described in detail in the data_records.md file. Reproducibility/: This directory contains the Jupyter (IPython) notebook and the sub-directories used by the notebook in order to reproduce the products in this project. background.md: Provides a brief summary of the underlying experiment and goals of this project. methods.md: Describes the means by which the data for this project was analyzed. data_records.md: Describes the various products generated by RNAseq_TopHat_Cufflinks_Workflow.ipynb, including describing the IPython notebook itself. |
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