Data from: Gene expression plasticity as a mechanism of coral adaptation to a variable environment

Kenkel CD, Matz MV

Date Published: November 11, 2016

DOI: http://dx.doi.org/10.5061/dryad.2bv13

 

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Title R script for statistical analyses
Downloaded 116 times
Description Annotated R script for completing statistical analyses as described in the publication (e.g. WGCNA, DAPC, etc).
Download WGCNA_DFA_final.R (36.36 Kb)
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Title R script for plots
Downloaded 32 times
Description Annotated R script for obtaining gene lists from gene ontology enrichement analyses (completed using the GO_MWU package - https://github.com/z0on/GO_MWU) and plotting heatmaps.
Download go_plotresults_versionCarl.R (5.105 Kb)
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Title Coral Host Physiological Trait Data
Downloaded 21 times
Description .csv file of physiological trait data for coral host samples, used as input for the WGCNA R script.
Download WGCNA_traitsHost.csv (4.742 Kb)
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Title Gene Ontology Annotations for Porites astreoides transcriptome
Downloaded 17 times
Description .tab file of GO term annotations for isogroups in the Porites astreoides transcriptome. Used as input for the statistical and plots R scripts.
Download past2digNvecManual_apr2014_iso2go_ckupdate.tab (812.5 Kb)
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Title DAPC assignments for host cellular response to stress genes
Downloaded 28 times
Description .csv file of DAPC assignments for environmental stress response genes - i.e. those annotated with the GO terms 'cellular response to stress' and 'ribosome biogenesis'. Used as input for statistical R script.
Download Host_IndividCoord_DFA_CRSgenes.csv (3.663 Kb)
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Title Standardized traits in coral host
Downloaded 17 times
Description .csv file of standardized gene expression and fitness-related traits (percent weight gain) for the coral host. Used to calculate the costs of expression plasticity using the selection gradient method. Used as input for the statistical R script.
Download PlasticityCosts.csv (3.724 Kb)
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Title Normalized expression data for ESR genes in the coral host
Downloaded 19 times
Description .csv file of normalized expression data by sample for genes annotated with either the 'cellular response to stress' or 'ribosome biogenesis' GO term. Used as input for R statistical script.
Download Host_annotESRgenes_CRSriboBiogen.csv (54.67 Kb)
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Title DAPC assignments for all Symbiodinium genes
Downloaded 18 times
Description .csv file of DAPC assignments for all high expression Symbiodinium genes. Used as input for statistical R script.
Download Sym_IndividCoord_DFA_1174genes.csv (1.212 Kb)
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Title DAPC assignments for all coral host genes
Downloaded 31 times
Description .csv file of DAPC assignments for all high expression coral host genes. Used as input for statistical R script.
Download Host_IndividCoord_DFA_7008genes.csv (1.215 Kb)
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Title Gene Ontology Annotations for Symbiodinium Clade A transcriptome (kb8)
Downloaded 17 times
Description .tab file of GO term annotations for isogroups in the Symbiodinium Clade A transcriptome (strain kb8). Used as input for the statistical and plots R scripts.
Download kb8_mar2014_iso2go.tab (1.499 Mb)
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Title Raw expression counts for coral host
Downloaded 37 times
Description Table of raw read count data for the coral host by sample (ii=inshore to inshore; io=inshore to offshore; oi=offshore to inshore; oo=offshore to offshore; number indicates genotype). Used as input for the R statistical script.
Download allcountsHostOnly_Bowtie2.txt (2.948 Mb)
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Title Raw expression counts for Symbiodinium
Downloaded 24 times
Description Table of raw read count data for in hospite Symbiodinium by sample (ii=inshore to inshore; io=inshore to offshore; oi=offshore to inshore; oo=offshore to offshore; number indicates genotype). Used as input for the R statistical script.
Download allcountsSymOnly_Bowtie2.txt (2.225 Mb)
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Title Gene Name Annotations for Porites astreoides transcriptome
Downloaded 13 times
Description .tab file of gene name annotations for isogroups in the Porites astreoides transcriptome. Used as input for the statistical and plots R scripts
Download past_apr2014_iso2gene.tab (1.034 Mb)
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Title Gene Name Annotations for Symbiodinium Clade A transcriptome (kb8)
Downloaded 15 times
Description .tab file of gene name annotations for isogroups in the Symbiodinium Clade A (strain kb8) transcriptome. Used as input for the statistical and plots R scripts
Download kb8_mar2014_iso2gene.tab (1.459 Mb)
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When using this data, please cite the original publication:

Kenkel CD, Matz MV (2016) Gene expression plasticity as a mechanism of coral adaptation to a variable environment. Nature Ecology & Evolution 1: 0014. http://dx.doi.org/10.1038/s41559-016-0014

Additionally, please cite the Dryad data package:

Kenkel CD, Matz MV (2016) Data from: Gene expression plasticity as a mechanism of coral adaptation to a variable environment. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.2bv13
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