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Sample GSM3813951 Query DataSets for GSM3813951
Status Public on Jun 10, 2020
Title 13-WGE200x-48h-1
Sample type SRA
 
Source name seed
Organism Glycine max
Characteristics cultivar: Harosoy63
treatment: WGE
hours after treatment: 48
tissue: seed
Extracted molecule total RNA
Extraction protocol Total RNA from soybean seeds was extracted using the Spectrum Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO, USA) following the manufacturer’s protocol with some modification as described previously (Farrell et al., 2017).
The mRNA stranded library prep kit from KAPA Biosystems and 750 ng of total RNA were used to build each library following manufacturers recommended protocol with nine cycles of PCR.
RNA-seq: 100 bp paired-end reads were generated with the Illumina HiSeq1500 system.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing QC checks were conducted upon receiving the raw data from the sequencing facility using FastQC software
Ribosomal RNA (rRNA) contamination, adapter sequences and/or low expressed genes were filtered out from the raw high-throughput RNA Sequencing data
clean reads were mapped/aligned to soybean (Glycine max) reference genome (Gmax_275_V2.0.fa, https://phytozome.jgi.doe.gov/pz/portal.html) using STAR RNA-seq Aligner with default parameters based on the current gene annotation
Only the paired mapped reads were considered for further analyses and the number of reads per gene was calculated using Feature Counts to count only reads which mapped concordantly
Differentially expressed genes (DEGs) were identified using DESeq2 package which is based in Negative Binomial Distribution
Multiple hypothesis correction was carried out to obtain an adjusted P value at 0.05 with Benjamini Hochberg procedure which is a powerful tool to decrease the false discovery rate (FDR). Principle component analysis, heatmap and clustering of the samples were also conducted to check the robustness of the analysis
Genome_build: Gmax_275_V2.0.fa, https://phytozome.jgi.doe.gov/pz/portal.html
Supplementary_files_format_and_content: Microsoft Excel Worksheet, DeSeq results annotated
 
Submission date May 23, 2019
Last update date Jun 11, 2020
Contact name Nik Kovinich
Organization name West Virginia University
Department Plant and Soil Sciences
Street address 1194 Evansdale Drive
City Morgantown
State/province WV
ZIP/Postal code 26506
Country USA
 
Platform ID GPL24802
Series (1)
GSE131686 Glyceollin transcription factor GmMYB29A2 is a regulator of soybean resistance to Phytophthora sojae
Relations
BioSample SAMN11836266
SRA SRX5887591

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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