Computational protocol: Effect of Cinnamaldehyde and Citral Combination on Transcriptional Profile, Growth, Oxidative Damage and Patulin Biosynthesis of Penicillium expansum

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Protocol publication

[…] Spores of P. expansum were inoculated in PDB medium supplemented with 0 or 1/2 MIC of Cin/Cit and cultured at 25°C, 120 rpm for 5 days. Each group has two biological replicates. The harvested mycelia were quickly frozen with liquid nitrogen for total RNAs preparation, RNA quality detection, cDNA libraries construction and RNA-seq, which was performed at Novogene Bioinformatics Technology Co., Ltd. (Beijing, China). Total RNA was extracted using TRIzol reagent (Invitrogen, United States) according to the manufacturer’s instruction and treated with RNase-free DNase I. The agarose gel electrophoresis, a NanoDrop®2000 spectrophotometer (Thermo Scientific, Wilmington, DE, United States), a Qubit®Fluorometer 2.0 (Life Technologies, Carlsbad, CA, United States) and an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, United States) were used to test the concentration and integrity of RNA samples (). The cDNA libraries were constructed according to previous reports and were sequenced on the Illumina HiSeq2000 platform (HiSeq2000, Illumina, San Diego, CA, United States, 2010) (; ). The resulting RNA-seq reads were mapped onto the reference genome of P. expansum Link isolate d1 from Israel (denoted as PEXP) using Tophat v2.0.12 (; ).Additionally, the followed analysis, including quantification of gene expression (HTSeq v0.6.1), identification of differentially expressed genes (DEGs) (DESeq v1.10.1), enrichment analysis of DEGs by GO enrichment analysis (GOSeq Release2.12) and KEGG pathways analysis (KOBAS v2.0), were carried out based on a previous report (). The RNA-Seq data have been deposited in the Genome Sequence Archive in BIG Data Center, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, with accession code CRA000582. […]

Pipeline specifications

Software tools TopHat, HTSeq, DESeq, GOseq, KOBAS
Databases KEGG BIG Data Center GSA
Application RNA-seq analysis
Organisms Penicillium expansum
Chemicals Amino Acids, Hydrogen Peroxide, Superoxides