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| Status |
Public on Jan 21, 2024 |
| Title |
Wild type, replicate 2 |
| Sample type |
SRA |
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| Source name |
Mycelium
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| Organism |
Fusarium fujikuroi |
| Characteristics |
tissue: Mycelium
cell line: IMI58289
cell type: Hyphae
genotype: wild type
treatment: Grown in dark
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| Growth protocol |
the strains were grown in 100 ml of DG medium in 500 ml Erlenmeyer flasks, inoculated with 1000000 conidia. The flasks were kept in total darkness for three days at 30°C in an orbital shaker (150 rpm). Then, the cultures were transferred to four 25-ml Petri dishes under safe red light and kept in static conditions in the dark for 240 min. Subsequently, mycelium was obtained by filtration, frozen immediately in liquid nitrogen, and stored at − 80 °C until RNA extraction
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA samples were extracted with Trizol (Invitrogen, Paisley, UK) from 150–200 mg of ground mycelia samples, using the protocol described by the manufacturer
RNA samples were sent for mass sequencing to LifeSequencing S. L. (Valencia, Spain). RIN values were above 8.5 in all the samples. Sequencing was carried out using the Illumina platform. Samples were sequenced on Illumina's NextSeq platform in 75 bp single read mode.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Raw reads for all samples were trimmed, filtered and quality controlled with AfterQC (Chen et al., 2017; doi:10.1186/s12859-017-1469-3)
Read mapping to the reference genome was performed using Star (Dobin et al. 2013)
The annotation used was the corresponding one from the EnsemblFungi database (https://fungi.ensembl.org) for F. fujikuroi IMI58289.
Mapped sequences were analyzed using SeqMonk (version 1.45.4, https://github.com/s-andrews/SeqMonk)
Quantification was performed using the Seqmonk RNAseq quantitation pipeline, merging transcripts and counting reads over exons.
Deseq2 tool (Love et al., 2014; doi:10.1186/s13059-014-0550-8), implemented in SeqMonk, which uses raw counts for quantitation, was used to compare among conditions.
Assembly: EF1.27
Supplementary files format and content: WT_dcl2_raw_counts.csv: Raw counts in Fusarium fujikuroi genes in wild type and dcl2 mutant, csv format
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| Submission date |
Jan 12, 2024 |
| Last update date |
Jan 21, 2024 |
| Contact name |
Javier Avalos |
| E-mail(s) |
[email protected]
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| Phone |
+34 954557110
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| Organization name |
Universidad de Sevilla
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| Department |
Genetica
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| Street address |
Av. Reina Mercedes sn
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| City |
Sevilla |
| ZIP/Postal code |
41012 |
| Country |
Spain |
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| Platform ID |
GPL24816 |
| Series (2) |
| GSE253159 |
Evidence of small interfering RNA in the fungus Fusarium fujikuroi (RNA-Seq) |
| GSE253166 |
Evidence of small interfering RNA in the fungus Fusarium fujikuroi |
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| Relations |
| BioSample |
SAMN39423393 |
| SRA |
SRX23203833 |
| 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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