Computational protocol: A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development

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Protocol publication

[…] To compare the arr1/10/12 triple mutant with the wild type, three-days-old seedlings were collected without any treatment. For cytokinin treatment, 10 µM 6-BA or an equal volume of ethanol was applied to each sample. RNA was isolated using RNeasy plant kit (Qiagen, cat #74904) and libraries were prepared by NeoPre Library Prep System (Illumina). Alignments were done by Tophat 2(v2.0.8, using TAIR10, Bowtie 2, and default parameters) and differential expression was called by CuffDiff (Cufflinks v2.1.1, using TAIR10 and default parameters). The significantly differentially expressed genes used 1.6-fold change and q-value <= 0.05 as cutoff. […]

Pipeline specifications

Software tools TopHat, Bowtie, Cufflinks
Databases TAIR
Application RNA-seq analysis
Organisms Arabidopsis thaliana