Computational protocol: Accumulation of high OPDA level correlates with reduced ROS and elevated GSH benefiting white cell survival in variegated leaves

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Protocol publication

[…] Harvested tissues were first ground in liquid nitrogen, and used to isolate RNA with Qiagen RNeasy kit (Qiagen). DNase I treatment was applied to remove any DNA contamination. The RNA samples were sent to Genomic Sciences Laboratory at North Carolina State University for Illumina sequencing. The sequencing reactions were run on the Illumina GAIIx with single-end 72 bp read or on the Illumina Hyseq 2000 with single-end 100 bp read. The Consensus Assessment of Sequence and Variation (CASAVA) software (Illumina) was used to remove adaptor sequences, nucleotide library indexes and generate fastq files. The sequence data was summarized in . For DEG analysis, the RNA-Seq reads were mapped to the E. aureum unique gene sequences from various types tissues of ‘Marble Queen’ and its green reversion ‘Jade’ in our previous study (NCBI Bioproject accession number PRJNA286034) by Bowtie. The differential expression analysis was conducted by edgeR with the false discovery rate (FDR) < 0.05. Reciprocal blast using BLASTX and TBLASTN approaches was conducted to search the ortholog gene contigs matching to Arabidopsis genes listed at TAIR v10 protein database with a maximum E value of 1e-5 and the best hit was assigned. […]

Pipeline specifications

Software tools BaseSpace, Bowtie, edgeR, BLASTX, TBLASTN
Databases TAIR
Applications RNA-seq analysis, Amino acid sequence alignment
Organisms Epipremnum aureum
Chemicals Glutathione