Data from: Gene expression associated with white syndromes in a reef building coral, Acropora hyacinthus

Wright RM, Aglyamova GV, Meyer E, Matz MV

Date Published: May 12, 2015

DOI: http://dx.doi.org/10.5061/dryad.8mr56

 

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Title Count data
Downloaded 12 times
Description Table of count data from processed reads. Columns are samples. Rows are genes.
Download 25july_diseasecounts.tab (5.069 Mb)
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Title DESeq2 script
Downloaded 50 times
Description DESeq2 script to analyze gene expression from count data. This script will call for the counts file.
Download deseq2_Ahya_Final.R (8.46 Kb)
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Title Principal coordinate analysis script
Downloaded 25 times
Description Script for principal coordinate analysis of gene expression data with the R package vegan. This script will call for variance stabilized data generated in DESeq2.
Download PCoA_Ahya_Final.R (2.426 Kb)
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Title Variance stabilized gene expression data and p-values
Downloaded 13 times
Description Variance stabilized gene expression and p-values were generated using the R package DESeq2. Row names are gene names. Column names are either sample names (columns 1-24) or p-values (columns 25-30). The letters following the p-value (pval or padj, for unadjusted and FDR corrected p-values respectively) indicate the contrast used to generate the pvalue: AH = ahead of the lesion to healthy, DA = disease to ahead of the lesion, DH = disease to healthy.
Download VSDandPVALS_disease.csv (22.59 Mb)
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Title WGCNA script
Downloaded 130 times
Description Script for network analysis of gene expression using the R package WGCNA. The script will require variance stabilized gene expression data for all samples and a table of trait values for each sample.
Download WGCNA_Ahya_Final.R (11.79 Kb)
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Title Variance stabilized gene expression data for WGCNA
Downloaded 24 times
Description Variance stabilized gene expression data for all samples from the top differentially expressed genes (unadjusted p-value < 0.1) for network analysis with the R package WGCNA. Rows are genes. Columns are samples.
Download genes4WGCNA.csv (2.834 Mb)
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Title Samples and traits for WGCNA
Downloaded 20 times
Description Table of traits for samples for network analysis with the R package WGCNA. Rows are samples. Columns are traits. Values are binary indicators of whether the sample is positive for that trait. Traits are AL, H, and D for the three disease states (ahead of the lesion, healthy, and diseased) and 1-16 for each genotype.
Download diseasetraits_reps.csv (1.051 Kb)
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Title Acropora hyacinthus transcriptome
Downloaded 11 times
Description The version of the transcriptome used for this analysis.
Download ahyac_jan2012.fasta (31.75 Mb)
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When using this data, please cite the original publication:

Wright RM, Aglyamova GV, Meyer E, Matz MV (2015) Gene expression associated with white syndromes in a reef building coral, Acropora hyacinthus. BMC Genomics 16: 371. http://dx.doi.org/10.1186/s12864-015-1540-2

Additionally, please cite the Dryad data package:

Wright RM, Aglyamova GV, Meyer E, Matz MV (2015) Data from: Gene expression associated with white syndromes in a reef building coral, Acropora hyacinthus. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.8mr56
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