|
| Status |
Public on Apr 30, 2019 |
| Title |
Intermediate line from location 4 |
| Sample type |
SRA |
| |
|
| Source name |
infected spikelet from soft red winter wheat head
|
| Organism |
Fusarium graminearum |
| Characteristics |
resistance level: intermediate
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 SMS229 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 |
| E-mail(s) |
santiagomideros@gmail.com
|
| 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 |
|
| Relations |
| BioSample |
SAMN09927126 |
| SRA |
SRX4649778 |
