|
| Status |
Public on Jun 01, 2018 |
| Title |
F_oxysporum_WT_Light_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Wild type after 1h light
|
| Organism |
Fusarium oxysporum f. sp. lycopersici |
| Characteristics |
strain: 4287
genotype: wild type
cell type: mycelium
|
| Treatment protocol |
Illumination was achieved with a set of four fluorescent tubes (Philips TL-D 18W/840) at a distance of ca. 60 cm, providing a light intensity of 0.25 m
|
| Growth protocol |
106 conidia were inoculated into 100 ml of DG medium in 500-ml Erlenmeyer flasks and incubated in the dark for three days in an orbital shaker. For illumination 25 ml samples of the cultures were transferred to Petri dishes under red safelight and incubated for one hour either in the dark or under white light The process with F. oxysporum was the same, except that the 3-day cultures were incubated in 145-mm Petri dishes with 80 ml of DGasn medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA samples were extracted with Trizol (Invitrogen, Paisley, UK) using the protocol described by the manufacturer
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
454 GS FLX |
| |
|
| Data processing |
Quality control was performed using the software packges FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read mapping to the reference genome was performed using Tophat (https://ccb.jhu.edu/software/tophat/index.shtml)
Transcript assembly was performed using Cufflinks and Cuffmerge (http://cole-trapnell-lab.github.io/cufflinks/)
Gene expression level measured in FPKM (fragments per kilobase of exon and million of mapped reads) was perfomed using Cufflinks and Cuffdiff
Subsequent data analysis and visualization was performed using the R bioconductor package cummeRbund (http://bioconductor.org/packages/release/bioc/html/cummeRbund.html)
Genome_build: EF1.27 (fusarium fujikuroi) and FO2.27 (fusarium oxysporum)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
|
| |
|
| Submission date |
Nov 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Javier Avalos |
| E-mail(s) |
avalos@us.es
|
| Phone |
+34954557110
|
| Organization name |
University of Seville
|
| Department |
Genetics
|
| Street address |
Av. Reina Mercedes sn
|
| City |
41012 |
| ZIP/Postal code |
41012 |
| Country |
Spain |
| |
|
| Platform ID |
GPL24306 |
| Series (1) |
| GSE107342 |
RNAseq analysis of the effects of light and the carS mutation in Fusarium fujikuroi and Fusarium oxysporum |
|
| Relations |
| BioSample |
SAMN08099140 |
| SRA |
SRX3422634 |
