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Sample GSM3634080 Query DataSets for GSM3634080
Status Public on Apr 30, 2019
Title Resistant line from location 4
Sample type SRA
Source name infected spikelet from soft red winter wheat head
Organism Fusarium graminearum
Characteristics resistance level: resistant
location: 4
Treatment protocol From one infected head for each variety, and at each location, the most diseased spikelet was placed in a 1.5mL micro-centrifuge tube containing 500µL of RNAlater (Sigma-Aldrich, St. Louis, Missouri) and kept at 4°C until arriving at the laboratory and then at -20°C until processing
Extracted molecule total RNA
Extraction protocol RNAs were extracted using a combination of TRIzol (ThermoFisher Scientific, Waltham, Massachusetts) and RNAeasy Min Elute Cleanup Kit (Qiagen, Hilden, Germany)
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
Description sample ID SMR201 collected in Savoy, IL
Data processing The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from each end of the fragments on a HiSeq 4000 using a HiSeq 4000 sequencing kit version 1.
Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina), which trims off adaptors and removes sequences less than 35 nt
Each sample's fastq file was run through Trimmomatic 0.36 to first remove any remaining standard Illumina TruSeq SE v3 adapters, then trim bases from both ends with quality scores below 28, and finally to remove reads shorter than 30 bp (parameters ILLUMINACLIP:$EBROOTTRIMMOMATIC/adapters/TruSeq3-SE.fa:2:15:10 LEADING:28 TRAILING:28 MINLEN:30)
Alignment was done to EnsemblFungi's Fusarium graminearum PH-1 genome (Assembly: GCA_900044135.1) using STAR (version 2.5.3a) [30] using parameters --sjdbGTFfeatureExon exon, --sjdbGTFtagExonParentGene gene_id and --sjdbOverhang 99.
Gene counts were generated using featureCounts in the subread package (version 1.5.2) using only uniquely aligned reads.
Genome_build: EnsemblFungi Fusarium graminearum PH-1
Supplementary_files_format_and_content: tab-delimited text files of raw counts per gene per sample were used directly in edgeR 3.20.0 for statistical analysis and thus are the "normalized" data.
Submission date Feb 27, 2019
Last update date May 01, 2019
Contact name Santiago Xavier Mideros
Phone 6073398711
Organization name University of Illinois at Urbana Champaign
Department Crop Sciences
Lab Mideros
Street address AW-101 Turner Hall / 1102 S. Goodwin Av.
City Urbana
State/province Illinois
ZIP/Postal code 61801
Country USA
Platform ID GPL24502
Series (1)
GSE127334 Field pathogenomics of Fusarium head blight reveals pathogen transcriptome differences due to host resistance
BioSample SAMN09927127
SRA SRX4649777

Supplementary file Size Download File type/resource
GSM3634080_SMR201_GTCCGCAC_L001_Aligned.sortedByCoord.out_featCounts.txt.gz 423.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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