Data from: Genome-wide transcriptional signatures of migratory flight activity in a globally invasive insect pest

Jones CM, Papanicolaou A, Mironidis GK, Vontas J, Yang Y, Lim KS, Singh KS, Oakeshott JG, Bass C, Chapman JW

Date Published: August 26, 2015

DOI: http://dx.doi.org/10.5061/dryad.bp7j7

 

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Title Total distance flown by individual adult Helicoverpa armigera on the flight mills
Downloaded 11 times
Description Flight mill data used in all figures and REML analyses. This data is used in Fig1B, Fig1C and FigS2. Column headings and data are as follows:- ID = the flight mill channel (A or B), year flown ('13' represents 2013), date flown (e.g. Nov13 = November 13th) and mill flown (e.g. _Ch7 = mill #7). origin = origin of the insect population. sex = male (m) or female (f). Total distance flown = the total distance (metres) each individual flew on the flight mill during the course of a single night as recorded by the tethered flight mill.
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Title RNAseq read count data from China Helicoverpa armigera
Downloaded 8 times
Description The data is a matrix of read counts generated from an RNAseq analysis of six samples of H. armigera. Each RNA sample was extracted from a pool of three whole individual insects. The first column contains the gene identification number. All other column headings represent the individual samples. AY = insects from Anyang. DF = insects from Dafeng. The data was used to determine differential gene expression using the open software packages edgeR and DEseq2.
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Title RNAseq read count data from Greek Helicoverpa armigera
Downloaded 5 times
Description The data is a matrix of read counts generated from an RNAseq analysis of six samples of H. armigera from Greece. Each RNA sample was extracted from a pool of three whole individual insects. The first column contains the gene identification number. All other column headings represent the individual samples. GR_S = short-distance flying insects from Northern Greece. GR_L = long-distance flying insects from Northern Greece. The data was used to determine differential gene expression using the open software packages edgeR and DEseq2.
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Title RNA-seq analysis of flight phenotypes of H. armigera - DEseq2 full output
Downloaded 35 times
Description Output from R package DEseq2 for China and Greece H. armigera RNAseq experiments analysing differential expression between flight phenotypes. Gene ID = gene identification number. baseMean = average of the normalised count values. log2FoldChange = estimated log fold change between sample groups (for China the estimate is measured against AY; for Greece the estimate is measured against GR_S). lfcSE = standard error estimate for logFC. p-value = evidence for an effect of treatment on expression. padj = multiple testing correction for p-value. 'NA' in the p-value or padj column indicates that the gene was excluded from the analysis due to no count data or an extreme outlier.
Download deseq2_full_output.xlsx (2.308 Mb)
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Title RNAseq analysis of H. armigera flight phenotypes - edgeR_full_output
Downloaded 33 times
Description Output from R package edgeR for China and Greece H. armigera RNAseq experiments analysing differential expression between flight phenotypes. Gene ID = gene identification number. logFC = estimated log fold change between sample groups (for China the estimate is measured against AY; for Greece the estimate is measured against GR_S). logCPM = log2 counts per million. p-value = evidence for an effect of treatment on expression. FDR = multiple testing correction for p-value. Note that the number of rows do not equate to the number of total estimated genes (17001). This is because data with less than 5 read counts across all samples are removed from the analysis.
Download edgeR_full_output.xlsx (1.721 Mb)
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Title Identified GO terms for Helicoverpa armigera genes
Downloaded 13 times
Description The file provides a list of GO-terms used in a functional enrichment analysis for genes involved in flight activity in Helicoverpa armigera. The list was generated using BLAST-2-GO. A total of 11316 genes (from a total of 17001) have identified GO-terms.
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Title Raw qPCR data for RNA-seq validation
Downloaded 34 times
Description Data file consists of two excel sheets. The first sheet labelled 'ct' contains all raw Ct values that informed the qPCR analysis. Column headings are gene IDs for that particular gene. Information on qPCR primers and efficiency can be found in the Supplementary information. 'Treatment' = phenotype tested. 'Biorep' = biological replicate. 'Techrep' = technical replicate. The second sheet ('validation') contains the fold-change comparisons that informed the RNA-seq validation analysis. Validations were performed for each software package - edgeR and DEseq2. Comparisons were made only in instances when the gene was significantly differentially expressed in the RNA-seq.
Download jones_mol_ecol_qpcr_ct.xlsx (16.30 Kb)
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When using this data, please cite the original publication:

Jones CM, Papanicolaou A, Mironidis GK, Vontas J, Yang Y, Lim KS, Oakeshott JG, Bass C, Chapman JW (2015) Genome-wide transcriptional signatures of migratory flight activity in a globally invasive insect pest. Molecular Ecology 24(19): 4901–4911. http://dx.doi.org/10.1111/mec.13362

Additionally, please cite the Dryad data package:

Jones CM, Papanicolaou A, Mironidis GK, Vontas J, Yang Y, Lim KS, Singh KS, Oakeshott JG, Bass C, Chapman JW (2015) Data from: Genome-wide transcriptional signatures of migratory flight activity in a globally invasive insect pest. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.bp7j7
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