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Sample GSM3717546 Query DataSets for GSM3717546
Status Public on Apr 26, 2019
Title 12C_Control_Resistant_Day11
Sample type SRA
Source name Leaves
Organism Glycine max
Characteristics protocol: Control
time point: Day11
tissue: Leaves
age: not applicable
genotype: LD12-15813Ra
Extracted molecule total RNA
Extraction protocol RNA was extracted from the leave samples from resistant and susceptible cultivars treated with no aphids, biotype 2: biotype1 collected at day 1 and no aphids, biotype 2: biotype1 and no aphids: biotype1 at day 11 using PureLink RNA mini kit (Invitrogen, USA). RNA samples were treated with TURBOTM DNase (Invitrogen, USA) to remove any DNA contamination following the manufacturer’s instructions. Assessment of the isolated RNA integrity was performed by 1% agarose gel electrophoresis, and RNA concentration was measured by Nanodrop 2000 (Thermo Fisher Scientific, USA). Three replicates from these treatments in resistant and susceptible cultivars were pooled in equimolar concentration.
RNAseq library construction was prepared using Illumina’s TruSeq Stranded mRNA Kit v1 (San Diego, CA). The libraries were quantified by QuBit dsDNA HS Assay (Life Technologies, Carlsbad, CA) and pooled in equimolar concentrations. The libraries were sequenced on an Illumina NextSeq 500 using a NextSeq 500/550 High Output Reagent Cartridge v2 (San Diego, CA) at 75 cycles.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 550
Data processing Quality control of reads was assessed using FastQC program (version 0.11.3) ( The FastQC results were visualized using MultiQC v1.3 9. Low quality bases (QC value < 20) and adapters were removed by trimming using the program Trimmomatic (version 0.36). The coding sequences (Gmax: Gmax_275_Wm82.a2.v1.transcript_primaryTranscriptOnly.fa.gz) were obtained from the Phytozome database and aligned using Salmon ver.0.9.1 accessed from Bioconda.
Genome_build: Gmax: Gmax_275_Wm82.a2.v1.transcript_primaryTranscriptOnly.fa.gz
Supplementary_files_format_and_content: tab-delimited matrix text file include transcript abundance values for each sample
Submission date Apr 11, 2019
Last update date May 11, 2019
Contact name Madhav P. Nepal
Organization name South Dakota State University
Department Biology and Microbiology
Lab Nepal Lab
Street address Northern Plains Biostress 249D
City Brookings
State/province South Dakota
ZIP/Postal code 57007
Country USA
Platform ID GPL26488
Series (1)
GSE129626 Characterization of induced susceptibility effects on soybean- soybean aphid interactions
BioSample SAMN11340097
SRA SRX5635787

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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