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| Status |
Public on Sep 01, 2019 |
| Title |
ΔFVEG_10494-6.4, 1.5 mM NO, rep 2 |
| Sample type |
SRA |
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| Source name |
PDB liquid culture
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| Organism |
Fusarium verticillioides |
| Characteristics |
strain: [delta] FVEG_10494-6.8
hours growth: 3 days + 30 min NO exposure
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| Treatment protocol |
Prior to harvesting samples, half of the cultures of each strain received 22.5 ul of 200 mM DETA NONOate (1.5 mM DETA NONOate final concentration in the 3 ml cultures) and were incubated an additional 30 min.
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| Growth protocol |
Three milliliters of PDB (potato dextrose broth; Neogen Food Safety, Lansing, MI, USA) in sterile snap-cap tubes, with caps loose, were inoculated with 1x10^6 F. verticillioides conidia and grown at 27 °C, 250 rpm for 3 days. Cultures of both FRC M-3125 and ΔFVEG_10494-6.4 were prepared.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For each treatment, 1 ml of culture was transferred to lysing matrix S tubes (MP Biomedicals, LLC, Santa Ana, CA, USA), centrifuged at 10,000 x g for 5 min at 4°C, and the supernatant discarded. Lysis buffer (PureLink® RNA Mini Kit, Thermo Fisher Scientific) was immediately added to the fungal pellets, and the samples were homogenized using the FastPrep-24™ 5G Instrument (MP Biomedicals) at a speed of 6 m/sec with two segments of homogenization for 30 seconds with a 1 min rest in between. The total RNA was extracted following the manufacturer’s instructions (PureLink® RNA Mini Kit, Thermo Fisher Scientific). Isolated RNA samples were DNase treated (TURBO DNA-free™ Kit, Thermo Fisher Scientific), tested by conventional PCR for the complete removal of DNA, and checked for quality (RNA integrity number > 6.0) using an Agilent 2100 Bioanalyzer (Agilent Technology, Waldbronn, Germany).
Twelve libraries (wild type and mutant ΔFVEG_10494-6.4 treated with and without 1.5 mM DETA NONOate for 30 min, with three biological replicates each) were prepared and sequenced on an Illumina NextSeq (75 Cycles) High Output Flow Cell (paired end, 75 bp read length) by the Georgia Genomics Facility at the University of Georgia.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
ΔFVEG_10494-6.4 NO-exposed, Rep2
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| Data processing |
FastQC
Removal of low quality reads (Phred score <20) and sequencing adapters using Trimmomatic 0.25
Bioconductor Rsubread align function for mapping filtered reads to the F. verticillioides genome
Read counting, normalization, and expression level (FPKM) calculations were executed using the featurecount function in Rsubread using the default settings.
Differential gene expression analysis was performed using edgeR and DESeq packages, by applying a false discovery rate threshold of < 0.05 for the adjusted p-value.
Genome_build: Fusarium verticillioides genome as downloaded from www.fungidb.org (Fusarium verticillioides_7600_3_supercontig)
Supplementary_files_format_and_content: FPKM values in tab delimited table format for all treatments and genes (.txt file)
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| Submission date |
Aug 20, 2018 |
| Last update date |
Sep 01, 2019 |
| Contact name |
Anthony E. Glenn |
| E-mail(s) |
anthony.glenn@usda.gov
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| Phone |
706-546-3119
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| Organization name |
USDA, ARS, USNPRC, R.B. Russell Research Center
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| Department |
Toxicology & Mycotoxin Research Unit
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| Street address |
950 College Station Rd
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| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30605 |
| Country |
USA |
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| Platform ID |
GPL25477 |
| Series (1) |
| GSE118800 |
Analysis of Fusarium verticillioides gene expression in response to nitric oxide (NO) |
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| Relations |
| BioSample |
SAMN09865700 |
| SRA |
SRX4579983 |
| 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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