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| Status |
Public on Jun 25, 2019 |
| Title |
M3125 OXD-1 |
| Sample type |
SRA |
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| Source name |
2-Oxindole treatement Rep1
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| Organism |
Fusarium verticillioides |
| Characteristics |
strain: Wild-type FRC M-3125
hours growth: 47 before induction + 1 after
treatment: 2-Oxindole
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| Treatment protocol |
At the final hour, 10 μL DMSO containing 100 μg of BOA, OXD, CMN, or CZX, or 10 μg of PA, or 40 μg of PB were was added to the respective treatments. Ten microliters of DMSO was added to control samples. All culture tubes were incubated for a final one-hour induction.
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| Growth protocol |
Two milliliters of PDB (potato dextrose broth; Neogen Food Safety, Lansing, MI, USA) cultures in sterile snap-cap tubes, with caps loose, were seeded with 10000 FRC M-3125 wild-type F. verticillioides conidia and grown at 27 °C, 250 rpm for 47 hours
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| Extracted molecule |
total RNA |
| Extraction protocol |
After the final hour, 1 mL liquid culture from each tube was pelleted by centrifugation at 8000 g for 5 min at 4 °C, resuspended in 1 mL lysis buffer, and transferred to lysing matrix D tubes (MP Biomedicals, LLC, Santa Ana, CA, USA). The tubes were homogenized with a FastPrep-24TM 5G instrument (MP Biomedicals) at 6 m/s with 2 pulses of 30 s and a 1 min intervening pause at room temperature. Total RNA was extracted from the homogenized samples with a PureLink® RNA Mini Kit (Thermo Fisher Scientific Inc., MA, USA) following the manufacturer’s protocol.
Sequencing libraries were constructed with Illumina Truseq DNA LT sample prep kit (Illumina Inc., San Diego, CA, USA) following the manufacturer’s protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
PDB liquid culture
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| Data processing |
Remove Adapter, Cutadapt 1.9.dev1, Trimmomatic 0.32
Tophat 2.0.13
Samtools 1.2
HTseq 0.6.1p1
DESeq2
Genome_build: Fusarium verticillioides 7600 RefSeq Genome
Supplementary_files_format_and_content: raw counts of sequencing reads for the genes of interest in .txt format. Gene identifiers correspond to FVEG locus tags (e.g., gene11400 is equivalent to FVEG_11400).
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| Submission date |
Jun 27, 2018 |
| Last update date |
Jun 26, 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 |
GPL19800 |
| Series (1) |
| GSE116351 |
Analysis of Fusarium verticillioides gene expression in response to lactam and lactone compounds |
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| Relations |
| BioSample |
SAMN09502812 |
| SRA |
SRX4314113 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3229701_OXD_1.txt.gz |
61.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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