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| Status |
Public on Apr 26, 2019 |
| Title |
5C_No Inducer_15 biotype1_Day11 |
| Sample type |
SRA |
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| Source name |
Leaves
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| Organism |
Glycine max |
| Characteristics |
protocol: No Inducer_ 15 biotype1
time point: Day11
tissue: Leaves
age: not applicable
genotype: LD12-15813Ra
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Data processing |
Quality control of reads was assessed using FastQC program (version 0.11.3) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). 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
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| Submission date |
Apr 11, 2019 |
| Last update date |
May 11, 2019 |
| Contact name |
Madhav P. Nepal |
| E-mail(s) |
madhav.nepal@sdstate.edu
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| Organization name |
South Dakota State University
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| Department |
Biology and Microbiology
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| Lab |
Nepal Lab
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| Street address |
Northern Plains Biostress 249D
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| City |
Brookings |
| State/province |
South Dakota |
| ZIP/Postal code |
57007 |
| Country |
USA |
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| Platform ID |
GPL26488 |
| Series (1) |
| GSE129626 |
Characterization of induced susceptibility effects on soybean- soybean aphid interactions |
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| Relations |
| BioSample |
SAMN11340101 |
| SRA |
SRX5635783 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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