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| Status |
Public on Jun 05, 2020 |
| Title |
WT-PN-BR2 |
| Sample type |
SRA |
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| Source name |
Fungal mycelia
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| Organism |
Fusarium graminearum |
| Characteristics |
genotype: WT
environmental conditions: preferred nutrient (PN)
timepoint: 24 hrs
sequencing: Illumina NextSeq
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| Growth protocol |
20,000 spores in 4 ml of PN medium were grown in 6-well plates (in the dark, at 28 degrees C, rotating at 160rpm); Samples destined for in NPN medium were then transferred to the NPN medium and grown for additional 24 hours under the same conditions. Mycelia was collected and frozen at -80 degrees C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Mycelia was ground in liquid nitrogen; total RNA was purified using Trizol extraction method and cleaned using Invitrogen Stratec kit (Ref# 1061100200).
RNA libraries were prepared for sequencing using standard Illumina protocols.
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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 read QC and trimming (CLC Genomics V12). Parameters: ambiguous limit 2, quality limit 0.05, min number of nucleotides in reads 20, discard short reads.
RNAseq Analysis function in CLC Genomics V12. Parameters: one reference sequence per transcript, no spike-in controls, mismatch cost 2, indel cost 3, length fraction 0.9, similarity fraction 0.8, auto-detect paired distances, strand specific - both, max number of hits for a read 10, do not count paired reads as two, expression value in unique counts.
DESeq2 to normalize unique gene read counts and to obtain differential expression.
Genome_build: The reference used was the CDS of genes predicted in SPRZ00000000 in the NCBI WGS. The CDS fasta is provided in the processed files.
Supplementary_files_format_and_content: CSV file provides unique gene reads for each sample originated from CLC Genomics RNAseq analysis (Column Headers = Strain-Condition-Replicate#; Row Headers = Gene IDs).
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| Submission date |
Dec 03, 2019 |
| Last update date |
Jun 05, 2020 |
| Contact name |
Kristina Shostak |
| Organization name |
Agriculture and Agri-Food Canada
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| Street address |
960 Carling Avenue
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| City |
Ottawa |
| ZIP/Postal code |
K1Y 4X2 |
| Country |
Canada |
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| Platform ID |
GPL27851 |
| Series (1) |
| GSE141331 |
Gene expression analysis by RNAseq in Fusarium graminearum WT, TRI6 mutant (∆tri6) and a mutant constitutively expressing TRI6 (∆tri6/TRI6). |
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| Relations |
| BioSample |
SAMN13470950 |
| SRA |
SRX7256712 |
| 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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