Data from: The influence of population structure on gene expression and flowering time variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae)

Kryvokhyzha D, Holm K, Chen J, Cornille A, Glémin S, Wright SI, Lagercrantz U, Lascoux M

Date Published: January 14, 2016

DOI: http://dx.doi.org/10.5061/dryad.q83pt

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Gene expression read counts for Capsella bursa-pastoris
Downloaded 24 times
Description This file contains expression values obtained using RNA-seq data for 24 accessions of Capsella bursa-pastoris. Read counting was performed using htseq-count program from HTSeq software v0.6.1 (Anders et al. 2014). Only reads mapped to non-overlapping feature positions were counted (htseq-count option: -m union).
Download Cbp_RNA-Seq_HTseq_counts.zip (999.7 Kb)
Details View File Details
Title R scripts: edgeR analysуs of Capsella bursa-pastoris
Downloaded 15 times
Description These scripts were used to perform differential gene expression analysis between and within the genetic groups (ASI, EUR, ME) of Capsella bursa-pastoris.
Download Cbp_RNA-Seq_edgeR.R.zip (3.499 Kb)
Details View File Details
Title R scripts: MCMCglmm analyses of Capsella bursa-pastoris
Downloaded 28 times
Description These scripts were used to perform correction for population structure in the analyses of gene expression and phenotypic variation in Capsella bursa-pastoris.
Download Cbp_RNA-Seq_MCMCglmm.R.zip (3.484 Kb)
Details View File Details
Title R script: Phenotypic and Environmental data analyses
Downloaded 12 times
Description This script was used to analyze phenotypic variation (flowering time and circadian rhythm) in Capsella bursa-pastoris and climatic characteristics of its collection sites.
Download Cbp_RNA-Seq_Phenotype-Environment.R.zip (2.398 Kb)
Details View File Details
Title Phylogentic relationships between accessions of Capsella bursa-pastoris
Downloaded 13 times
Description These phylogenetic trees were reconstructed using the GTRGAMMA model in RAxML v8.2.4 (Stamatakis et al. 2012)⁠ for 21 and 263 accessions that had SNPs data available (Cornille et al. 2015). A random tree was generated using the rcoal function from the ape package in R (Paradis et al. 2004)
Download Cbp_RNA-Seq_RAxML_Trees_GBS_nwk.zip (6.816 Kb)
Details View File Details

When using this data, please cite the original publication:

Kryvokhyzha D, Holm K, Chen J, Cornille A, Glémin S, Wright SI, Lagercrantz U, Lascoux M (2016) The influence of population structure on gene expression and flowering time variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae). Molecular Ecology 25(5): 1106–1121. http://dx.doi.org/10.1111/mec.13537

Additionally, please cite the Dryad data package:

Kryvokhyzha D, Holm K, Chen J, Cornille A, Glémin S, Wright SI, Lagercrantz U, Lascoux M (2016) Data from: The influence of population structure on gene expression and flowering time variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.q83pt
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: