|
|
GEO help: Mouse over screen elements for information. |
|
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 Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
|