|
| Status |
Public on Mar 18, 2019 |
| Title |
resistant soybean stem 96 hours post infection biological replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
resistant soybean stem 96 hours post infection
|
| Organism |
Sclerotinia sclerotiorum |
| Characteristics |
soybean plant phenotype: resistant
infection: S. sclerotiorum (fungal pathogen)
fungal condition: In planta
time: 96hr hpi
tissue: stem tissues and fungal material
|
| Treatment protocol |
Inoculations were performed using the cut petiole method as described by (Ranjan et al. 2017). Plant tissue was sampled by cutting horizontally above and below (1.5 cm) the node of the first trifoliate with a clean straight-edge razor. Tissue samples were collected at 24, 48, and 96 h post inoculation (hpi) and immediately frozen in liquid nitrogen prior to RNA extraction. As a control, Sclerotinia sclerotiorum strain 1980 cultures were grown on a shaker in glucose minimal media for 48 hours (150 rpm, 25℃).
|
| Growth protocol |
Soybean seedlings and plants were maintained in the greenhouse or growth chamber at 24 ± 2◦C with 16 h light/8 h dark photoperiod cycle. S. sclerotiorum strain 1980 was grown at room temperature on potato dextrose agar (PDA) for inoculations. Culture control (P1-3) was grown at room temperature in glucose minimal media (GMM).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the stem tissues and fungal material using a Trizol protocol. Samples were cleaned using the RNeasy Plant Mini Kit protocol (RNeasy Plant Mini Kit, Qiagen, Hilden, Germany). RNA concentration and purity were determined by Nanodrop and sample quality was assessed using an Agilent Bioanalyzer 2100 and a RNA 6000 Nano Kit.
RNA from each sample was randomly fragmented, and individually indexed libraries were prepared using the TruSeq RNA Sample Preparation v2 kit according to the manufacturer’s instructions protocol. Library was quantified with Qubit HS DNA kit. The quality of the library was checked with an Agilent Bioanalyzer 2100 and an Agilent DNA 1000 kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
S5-I
|
| Data processing |
The raw sequence reads were mapped to the genome using Subjunc aligner from Subread. The alignment bam files were compared against the gene annotation GFF file, and raw counts for each gene were generated using the featureCounts tool from subread.
Next, we performed additional QC at gene level, including number of genes detected, percentage of reads belonging to the top genes, normalization for RNA composition, and grouping and correlation between samples. Click here to view full QC report at gene level.
The raw counts data were normalized using voom method from the R Limma package, then used for differential expression analysis. See section 3 above for further technical details.
Based on expression changes, we further carried out analyses to detect enriched functions
Genome_build: The fungal genome, gene annotations, and mitochondrial genome were provided by the Broad Institute (INSDC: AAGT00000000.1 and KT283062.1).
Supplementary_files_format_and_content: comma-delimited text files include RPKM values for each Sample
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| |
|
| Submission date |
Oct 30, 2018 |
| Last update date |
Mar 18, 2019 |
| Contact name |
Mehdi Kabbage |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Wisconsin Madison
|
| Department |
Department of Plant Pathology
|
| Lab |
583 Russell Labs 1630 Linden Dr.
|
| Street address |
Department of Plant Pathology, 583 Russell Labs 1630 Linden Dr
|
| City |
Madison |
| State/province |
Wisconsin |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL20037 |
| Series (1) |
| GSE121983 |
Global transcriptome analysis of Sclerotinia sclerotiorum following infection of resistant and susceptible soybean lines |
|
| Relations |
| BioSample |
SAMN10349347 |
| SRA |
SRX4957923 |
