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Sample GSM4832046

Query DataSets for GSM4832046

Status

Public on Jan 15, 2021

Title

WT_R2_15

Sample type

SRA

Source name

Wild type 15 min illumination

Organism

Fusarium fujikuroi

Characteristics

strain: FKMC1995
genotype/variation: wild type
treatment: 15 min illumination
tissue: mycelium

Treatment protocol

Illumination was provided by a set of four fluorescent tubes (Philips TL-D 18 W/840) at a distance of 60 cm, yielding a light intensity of 7 W/m2.

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, the Petri dishes were either kept in the dark or illuminated for 15, 60, or 240 min.

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

Illumina NextSeq 500

Description

Wild type 15 min illumination, replicate 2

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 Tophat 2.1.1 (https://ccb.jhu.edu/software/tophat/index.shtml)
Transcript assembly was performed using Cufflinks and Cuffmerge (Roberts, 2011; doi:10.1093/bioinformatics/btr355. http://cole-trapnell-lab.github.io/cufflinks/)
Mapped sequences were analyzed using SeqMonk (version 1.45.4, https://github.com/s-andrews/SeqMonk)
Quantification was performed using the RNAseq quantitation pipeline with the improved mRNA annotation generated by Cuffmerge, merging transcripts and counting reads over exons.
Deseq2 tool (Love et al., 2014; doi:10.1186/s13059-014-0550-8), implemented in SeqMonk, which needs raw counts for quantitation, was used to compare among conditions.
Genome_build: FMJU01;
https://www.ebi.ac.uk/ena/browser/view/FMJU01000001-FMJU01000086
Supplementary_files_format_and_content: Processed data are described in a single tab-delimited text file that includes raw counts for all samples, indicating probe, chromosome, start and end positions, and feature. Transcripts with no equivalent in FFUJ annotation are indicated as "null"

Submission date

Oct 19, 2020

Last update date

Jan 15, 2021

Contact name

Javier Avalos

E-mail(s)

[email protected]

Phone

+34954557110

Organization name

University of Seville