Exchange of molecular and cellular information: a hybrid model that integrates stem cell divisions and key regulatory interactions [an3]

We performed a transcriptome analysis on the meristematic root tissue from the loss-of-function line an3 and WT plants. Overall design: Three biological replicates of an3 and WT seeds were plated. After 5 days of growth, ~5 mm of an3 and WT root tips were collected. RNA was extracted using the Qiagen RNeasy Micro kit and libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs). Libraries were sequenced on an Illumina HiSeq 2500 with 100 bp single-end reads. Gene expression analysis of raw RNA-seq data was performed using the TuxNet interface (Spurney et al, 2019). Specifically, TuxNet uses ea-utils fastq-mcf (Aronesty, 2011, Aronesty, 2013) for preprocessing, hisat2 (Kim et al., 2015) for genome alignment, and Cufflinks (Trapnell et al., 2012) for differential expression analysis.