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| Status |
Public on Sep 28, 2017 |
| Title |
F. fujikuroi FSU48 in planta |
| Sample type |
SRA |
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| Source name |
in planta, rice, 7 dpi
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| Organism |
Fusarium fujikuroi |
| Characteristics |
strain: FSU48
genotype: wild type
dpi: 7
culture condition: in planta, rice, 7 dpi
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| Growth protocol |
RNA was isolated from lyophilized mycelia grown before in liqid synthetic media with 6 mM or 60 mM glutamine for 3 days or from lyophilized infected rice roots after 7 days post infection.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent. The DNA was removed using DNAse I (Roche Diagnostics GmbH, Mannheim, Germany). RNA quality and concentration was measured with an Bioanalyzer (Agilent Technologies Deutschland, Böblingen, Germany).
Illumina TruSeq RNA Library
Total RNA was sequenced using Illumina HiSeq 2000 technology by BGI Tech Solutions (Hong Kong) Co., Limited.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Ffuj_FSU48_fpkm.txt
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| Data processing |
RNA-seq reads were mapped on the reference genomes using tophat2 (v2.0.8).
The interval for allowed intron lengths were set to min 20 nt and max 1 kb (Kim, 2013, Trapnell et al., 2009).
Cufflinks was used to determine the abundance of transcripts in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) and calculated differentially expressed genes using cuffdiff (Trapnell et al., ,2012, Trapnell et al., 2010).
The gene models were included as raw junctions. Genes with a minimum of fourfold increase or decrease in expression (|log2 of the FPKM values +1| ≥ 2) between the two experimental conditions were considered as regulated.
Genome_build: F. fujikuroi IMI58289 : http://www.ebi.ac.uk/ena/data/view/PRJEB185; Further 9 strains: http://www.ebi.ac.uk/ena/data/view/PRJEB14872
Supplementary_files_format_and_content: tab-delimited text files holding FPKM values for each sample
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| Submission date |
Nov 03, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ulrich Guldener |
| E-mail(s) |
[email protected]
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| Organization name |
Technische Universität München
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| Department |
Chair of genome-oriented bioinformatics
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| Street address |
Maximus-von-Imhof-Forum 3
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| City |
Freising |
| State/province |
Bavaria |
| ZIP/Postal code |
D-85354 |
| Country |
Germany |
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| Platform ID |
GPL22633 |
| Series (1) |
| GSE89480 |
Expression profiles of nine Fusarium fujikuroi strains revealed common and different sets of up-regulated genes |
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| Relations |
| BioSample |
SAMN05970489 |
| SRA |
SRX2323733 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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