Computational protocol: Transcriptomic Analysis of Gibberellin- and Paclobutrazol-Treated Rice Seedlings under Submergence

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Protocol publication

[…] Prior to assembly, low-quality reads, including reads containing sequencing adaptors or sequencing primer or nucleotide with q quality score < 20, were removed. The raw sequence data have been submitted to the NCBI Short Read Archive with accession number GSE104035. The obtained clean reads were mapped to the rice reference genome in rice genome annotation project database: (ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/) using the Tophat package. The aligned read files were processed by Cufflinks, which uses the normalized RNA-seq fragment counts to measure the relative abundances of the transcripts. The unit of measurement is Fragment per Kilobase of exon per Million fragments mapped (FPKM). Cufflink was used to de novo assemble the transcriptome. Only the comparisons with a “q value” less than 0.01 and status marked as “OK” in the Cuffdiff output were regarded as showing differential expression. […]

Pipeline specifications

Software tools TopHat, Cufflinks
Databases RGAP
Application RNA-seq analysis
Organisms Oryza sativa
Chemicals Ethanol