Data from: A unique ecological niche fosters hybridization of oak-tree and vineyard isolates of Saccharomyces cerevisiae.

Clowers KJ, Will JL, Gasch AP

Date Published: October 29, 2015

DOI: http://dx.doi.org/10.5061/dryad.bt5v6

 

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Title DC6.vcf
Downloaded 8 times
Description SNPs identified in cherry strain DC 6 using GATK. SNPs were called on both DC 6 and DC 16, then sites for each strain were separated, and all non-SNP positions removed using VCFtools.
Download DCM6.PASS_SNPs.NonREF.recode.vcf (6.465 Mb)
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Title DC16.vcf
Downloaded 6 times
Description SNPs identified in cherry strain DC 16 using GATK. SNPs were called on both DC 6 and DC 16, then sites for each strain were separated, and all non-SNP positions removed using VCFtools.
Download DCM16.PASS_SNPs.NonREF.recode.vcf (6.752 Mb)
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Title RNAseqCounts
Downloaded 8 times
Description Read counts for each gene across all strains analyzed in EdgeR.
Download Counts.txt (336.2 Kb)
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Title OakvVintopTags
Downloaded 4 times
Description EdgeR output for differentially expressed genes in oak versus vineyard strains.
Download OakvVintopTags.txt (646.7 Kb)
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Title DCtopTags
Downloaded 5 times
Description EdgeR output for DC-specific differentially expressed genes.
Download DCtopTags.txt (643.7 Kb)
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Title DCvOaktopTags
Downloaded 11 times
Description EdgeR output for differentially expressed genes in DC versus oak strains.
Download DCvOaktopTags.txt (641.8 Kb)
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Title DCvVintopTags
Downloaded 5 times
Description EdgeR output for differentially expressed genes in DC versus vineyard strains.
Download DCvVintopTags.txt (639.0 Kb)
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Title PCAsnps
Downloaded 8 times
Description VCF file containing all of the genotype data used for PCA.
Download 25Strains_latest_snp_R64-1-1_NonREF.recode.vcf (137.5 Mb)
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Title PCAmap File
Downloaded 4 times
Description map file created for PCA.
Download 25Strains.map (4.280 Mb)
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Title PCA ped file
Downloaded 6 times
Description ped file used for PCA
Download 25Strains.ped (20.57 Mb)
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Title PCAraw
Downloaded 4 times
Description raw file for PCA analysis
Download 25Strains.raw (12.68 Mb)
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Title Ch4 alignment
Downloaded 4 times
Description Alignment file of Chromosome 4 sanger sequencing
Download Ch4.nex (57.82 Kb)
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Title Chr4 tree file
Downloaded 4 times
Description Mr. Bayes tree file for Chromosome 4
Download Ch4.nex.con.tre (18.26 Kb)
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Title Ch9 alignment
Downloaded 6 times
Description Alignment file of Chromosome 9 sanger sequencing
Download Ch9.nex (33.55 Kb)
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Title Ch10 alignment
Downloaded 7 times
Description Alignment file of Chromosome 10 sanger sequencing
Download Ch10.nex (30.69 Kb)
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Title Ch9 tree file
Downloaded 4 times
Description MrBayes tree file for Chromosome 9
Download Ch9.nex.con.tre (16.59 Kb)
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Title Ch10 tree file
Downloaded 6 times
Description MrBayes tree file for Chromosome 10
Download Ch10.nex.con.tre (17.58 Kb)
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When using this data, please cite the original publication:

Clowers KJ, Will JL, Gasch AP (2015) A unique ecological niche fosters hybridization of oak-tree and vineyard isolates of Saccharomyces cerevisiae. Molecular Ecology 24(23): 5886–5898. http://dx.doi.org/10.1111/mec.13439

Additionally, please cite the Dryad data package:

Clowers KJ, Will JL, Gasch AP (2015) Data from: A unique ecological niche fosters hybridization of oak-tree and vineyard isolates of Saccharomyces cerevisiae. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.bt5v6
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