Comment[ArrayExpressAccession] E-GEOD-59875 MAGE-TAB Version 1.1 Public Release Date 2014-07-30 Investigation Title Transcriptomics of weed stress in soybean Comment[Submitted Name] Transcriptomics of weed stress in soybean Experiment Description Research conducted, including the rationale: Weeds reduce yield in soybeans through incompletely defined mechanisms. The effects of weeds on the soybean transcriptome were evaluated in field conditions during four separate gR1.fastqing seasons. Methods: RNASeq data were collected from 6 biological samples of soybeans gR1.fastqing with or without weeds. Weed species and the methods to maintain weed free controls varied between years to mitigate treatment effects and to allow detection of general soybeans weed responses. Key results: Soybean plants were not visibly nutrient or water stressed. We identified 55 consistently down-regulated genes in weedy plots. Many of the down-regulated genes were heat shock genes. Fourteen genes were consistently up-regulated. Several transcription factors including a PHYTOCHROME INTERACTING FACTOR 3-like gene (PIF3) were included among the up-regulated genes. Gene set enrichment analysis indicated roles for increased oxidative stress and jasmonic acid signaling responses during weed stress. Main conclusion: The relationship of this weed-induced PIF3 gene to genes involved in shade avoidance responses in arabidopsis provide evidence that this gene may be important in the response of soybean to weeds. These results suggest the weed-induced PIF3 gene will be a target for manipulating weed tolerance in soybean. Samples were collected from two treatments ("Control" and "Weedy") with six biological replicates (2008, 2009, and twop each for 2010 and 2011) for each treatment. Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Horvath Horvath Clay Person First Name David David Sharon Person Email horvathd@fargo.ars.usda.gov Person Affiliation US Dept. Agriculture Person Address Agr. Research Service, US Dept. Agriculture, 1605 Albrecht Blvd, Fargo, ND, USA Person Roles submitter Protocol Name P-GSE59875-4 P-GSE59875-1 P-GSE59875-3 P-GSE59875-2 Protocol Description Raw sequence reads were checked for quality using the FastQC0.10.0 program and quality trimmed using the Sickle-quality-base-triming program in the iPlant discovery environment with the parameters minimum quality = 20 and minimum number of bases = 70. The Tuxedo Suite (Tophat 1.0, Cufflinks 1.0 and Cuffdiff 1.0 for Single End reads) were used to map the quality trimmed sequences to the Glycine Max genome (Phytozome 9.0) in the iPlant archive (for only the first paired end reads since the quality of the second end was significantly less good). The resulting FPKM values from the Cufflinks output files (genes.fpkm_tracking) were placed in a single file and those that matched known soybean gene models were kept. FPKM values were log transformed (for use in follow-on programs to assess biological relevance). Genome_build: Glycine Max genome (Phytozome 9.0) Supplementary_files_format_and_content: Data table containing gene model, Protien name as indicated by most similar arabidopsis annotation, Most similar arabidopsis gene model name based on Phytozome 9.0 gene model annotation, Log2 transformed FPKM (fragments per kilobase per million reads) vales for indicated library, Average log ratio of the expression (weedy minus control) for the indicated year, P value as generated by CuffDiff program for weedy verses control from the two samples collected from indicated year Q value as generated by CuffDiff program for weedy verses control from the two samples collected from indicated year, and Functional annotation assigned to the gene model based on the Phytozome 9.0 database. plants were either grown with various weeds (see "Weedy" treatment conditions in metaflie) or under weed free conditions (see "Control" conditions in metafile) RNA extraction was performed by grinding approximately 0.1 grams of frozen tissue in liquid nitrogen to a fine powder, and adding 1 ml Trizol reagent (Ambion/Life Technologies). Chloroform:Isoamyl (24:1) was added to the Trizol/tissue mixture, centrifuged, and RNA was extracted from the resulting supernatant using an RNeasy Plant Mini kit (Qiagen). Quality control was assessed using a nanodrop bioanalyzer on the RNA setting. cDNA libraries were created following the Illumina TruSeq RNA Sample Preparation kit (Illumina). In short, 4000 ng of RNA was purified and fragmented into mRNA, followed by first and second strand cDNA synthesis. End repair and adenylation of 3’ ends preceded adapter ligation and PCR amplification. Library quality was assessed using an Agilent Bioanalyzer, and quantified for pooling by qRT-PCR using the PhiX Control Kit v2 according to manufacturer specifications. Libraries were paired-end sequenced on an Illumina HiSeq2000. Soybean were grown to the V3 stage in field conditions near Brookings SDl. Soil consistes of loess over glacial outwash, and the soil series is Brandt silty clay loam. Protocol Type normalization data transformation protocol sample treatment protocol nucleic acid library construction protocol growth protocol Experimental Factor Name SAMPLING DATE TEMPERATURE AT SAMPLING CUMMULATIVE PRECIPITATION AT SAMPLING TREATMENT R1.FASTQ SPACING Experimental Factor Type sampling date temperature at sampling cummulative precipitation at sampling treatment r1.fastq spacing Comment[SecondaryAccession] GSE59875 Comment[GEOReleaseDate] 2014-07-30 Comment[ArrayExpressSubmissionDate] 2014-07-29 Comment[GEOLastUpdateDate] 2014-08-01 Comment[AEExperimentType] RNA-seq of coding RNA Comment[AdditionalFile:Data1] GSE59875_supplemental_table_1.txt Comment[SecondaryAccession] SRP045061 Comment[SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/SRR1531418-SRR1531429 SDRF File E-GEOD-59875.sdrf.txt