Data from: Genome-wide association study of Arabidopsis thaliana leaf microbial community

Horton MW, Bodenhausen N, Beilsmith K, Meng D, Muegge BD, Subramanian S, Vetter MM, Vilhjálmsson BJ, Nordborg M, Gordon JI, Bergelson J

Date Published: November 13, 2014

DOI: http://dx.doi.org/10.5061/dryad.8sm01

 

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Title GWAS Results, PCA
Downloaded 23 times
Description Results from GWAS of eigenvectors (PCs) 1-5, after PCA of the bacterial and (separately) the fungal community. This tarball includes 'reports' (e.g. the top SNPs after GWAS), image files (manhattan plots), and the top GO-terms enriched in these GWAS results. The Methods section of the paper describes the procedure. Please note that files labeled '16S' correspond to the bacterial community, while files labeled 'ITS' correspond to the fungal community.
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Title GWAS Results, CCA
Downloaded 8 times
Description Results from GWAS of eigenvectors (CCAs) 1-5, after CCA of the bacterial and (separately) the fungal community. This tarball includes 'reports' (e.g. the top SNPs after GWAS), image files (manhattan plots), and the top GO-terms enriched in these GWAS results. The Methods section of the paper describes the procedure. Please note that files labeled '16S' correspond to the bacterial community, while files labeled 'ITS' correspond to the fungal community.
Download cca.tgz (1.934 Mb)
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Title GWAS Results, DCA
Downloaded 9 times
Description Results from GWAS of eigenvectors (DCAs) 1-4, after DCA of the bacterial and (separately) the fungal community. This tarball includes 'reports' (e.g. the top SNPs after GWAS), image files (manhattan plots), and the top GO-terms enriched in these GWAS results. The Methods section of the manuscript describes the procedure. Please note that 'decorana' (vegan's function, which was used for DCA) only returns 4 axes. Please note that files labeled '16S' correspond to the bacterial community, while files labeled 'ITS' correspond to the fungal community.
Download dca.tgz (840.8 Kb)
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Title GWAS Results, Presence-Absence (0/1) of Individual OTUs.
Downloaded 11 times
Description The presence or absence (0/1) of individual OTUs were used as phenotypes in GWAS. The Methods section of the paper describes the procedure. Please note that files labeled '16S' correspond to the bacterial community, while files labeled 'ITS' correspond to the fungal community.
Download pres.tgz (34.22 Mb)
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Title GWAS Results, Abundance (Sqrt(x)) of Individual OTUs
Downloaded 12 times
Description The square-root transformed abundances of individual OTUs were used as phenotypes in GWAS. The Methods section of the paper describes the procedure. Please note that files labeled '16S' correspond to the bacterial community, while files labeled 'ITS' correspond to the fungal community.
Download sqrt.tgz (48.94 Mb)
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Title GWAS Results, Individual OTUs (results from P/A and Sqrt(x) combined)
Downloaded 9 times
Description The presence vs. absence (0/1) of individual OTUs were used as phenotypes in GWAS. In separate analyses, the abundance (sqrt(x)) of individual OTUs were also used as phenotypes. These results (p-values) were combined using Brown's (1975) approach. The Methods section of the paper describes the procedure. Please note that files labeled '16S' correspond to the bacterial community, while files labeled 'ITS' correspond to the fungal community.
Download combined.tgz (39.48 Mb)
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When using this data, please cite the original publication:

Horton MW, Bodenhausen N, Beilsmith K, Meng D, Muegge BD, Subramanian S, Vetter MM, Vilhjálmsson BJ, Nordborg M, Gordon JI, Bergelson J (2014) Genome-wide association study of Arabidopsis thaliana leaf microbial community. Nature Communications 5: 5320. http://dx.doi.org/10.1038/ncomms6320

Additionally, please cite the Dryad data package:

Horton MW, Bodenhausen N, Beilsmith K, Meng D, Muegge BD, Subramanian S, Vetter MM, Vilhjálmsson BJ, Nordborg M, Gordon JI, Bergelson J (2014) Data from: Genome-wide association study of Arabidopsis thaliana leaf microbial community. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.8sm01
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