Data from: Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative

Wagner MR, Lundberg DS, Coleman-Derr D, Tringe SG, Dangl JL, Mitchell-Olds T

Date Published: November 13, 2014

DOI: http://dx.doi.org/10.5061/dryad.1t6s5.2

 

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 Plant data: sterilized field soil treatments
Downloaded 18 times
Description Plant pedigree information, phenotype data, and fitness data from greenhouse experiment investigating effects of 4 different sterilized field soils. "Block" = experimental block; "Genotype" = genotype code; "Subsp" = Subspecies code: W for west, E for east; "Treatment" = origin of sterilized field soil; "FLT" = flowering time (days); "elong" = elongation rate (mm/day); "HAF" = height at flowering (mm); "Leafper" = number of leaves per mm stem; "NFr" = number of fruits
Download a_final.txt (14.53 Kb)
Details View File Details
Title Plant data: microbial community treatments
Downloaded 16 times
Description Plant pedigree information, phenotype data, and fitness data from greenhouse experiment investigating effects of 4 different soil microbial communities. "Block" = experimental block; "Genotype" = genotype code; "Subsp" = Subspecies code: W for west, E for east; "Treatment" = origin of soil microbial community; "FLT" = flowering time (days); "elong" = elongation rate (mm/day); "HAF" = height at flowering (mm); "Leafper" = number of leaves per mm stem; "NFr" = number of fruits
Download b_final.txt (18.98 Kb)
Details View File Details
Title Key to soil sample IDs
Downloaded 15 times
Description Soil sample-level metadata. "SampleID" = unique identifier for soil samples (JGI notation). "Plant_ID" = unique identifier for soil samples (Duke notation). "Site" = field site of origin. "oldPlate" = plate identifier (Duke notation). "newPlate" = plate identifier (JGI notation). "Year" = year of soil collection
Download SMDsoils.txt (937 bytes)
Details View File Details
Title 16S gene copy number estimates
Downloaded 17 times
Description 16S gene copy number estimates for OTUs generated using corrected bioinformatics pipeline. OTUs with no available estimates were assigned the mean copy number of 2.7175
Download soil_otu_CN_v2.txt (819.5 Kb)
Details View File Details
Title soil OTU table (rarefied)
Downloaded 18 times
Description Soil OTU table rarefied to 40,000 reads per sample, used for all analyses in the publication (Wagner et al. 2014 Ecology Letters). This table contains only "reproducible" OTUs that had at least 25 reads in at least 5 samples BEFORE rarefaction (note that this thresholding step was performed on a larger dataset that included hundreds of samples, not yet published). First column contains unique identifiers of observed OTUs. Other columns contain the number of reads for each OTU in each soil sample after rarefaction.
Download soil_otu_table_rare_40k_v2.txt (524.5 Kb)
Details View File Details
Title soil OTU table
Downloaded 20 times
Description Unrarefied soil OTU table. This table contains only "reproducible" OTUs that had at least 25 reads in at least 5 samples (note that this thresholding step was performed on a larger dataset that included hundreds of samples, not yet published). First column contains unique identifiers of observed OTUs. Other columns contain the number of reads for each OTU in each soil sample. This file was the input leading to the rarefied dataset ('soil_otu_table_rare40k.txt') used for all downstream analyses in the publication.
Download soil_otu_table_v2.txt (349.1 Kb)
Details View File Details
Title OTU taxonomy
Downloaded 17 times
Description Contains taxonomic designations for OTUs
Download OMD_v2.txt (3.409 Mb)
Details View File Details
Title README
Downloaded 11 times
Download README_v2.rtf (3.158 Kb)
Details View File Details

When using this data, please cite the original publication:

Wagner MR, Lundberg DS, Coleman-Derr D, Tringe SG, Dangl JL, Mitchell-Olds T (2014) Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecology Letters 17(6): 717-726. http://dx.doi.org/10.1111/ele.12276

Additionally, please cite the Dryad data package:

Wagner MR, Lundberg DS, Coleman-Derr D, Tringe SG, Dangl JL, Mitchell-Olds T (2014) Data from: Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.1t6s5.2
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Version History

Item Version Date Summary

* Selected Version

Search for data

Be part of Dryad

We encourage organizations to: