DOI: 10.5061/dryad.cz8w9gj6n
title: Data for: Differentially expressed genes comparing WT plants vs xal1-2

description: The balance between cell growth, proliferation, and differentiation rates
 emerges from gene regulatory networks coupled to various signal
 transduction pathways, including reactive oxygen species (ROS) and
 transcription factors (FTs), enabling developmental responses to
 environmental cues. The Arabidopsis thaliana's primary root has
 become a valuable system for unraveling such networks. Recently, the role
 of transcription factors mediating ROS's inhibition of primary root
 growth has begun to be characterized. This study demonstrates that the
 MADS-box transcription factor XAANTAL1 (XAL1) is an essential regulator of
 hydrogen peroxide (H2O2) in primary root growth and root stem cell niche
 identity. Interestingly, our findings suggest that XAL1 acts as a positive
 regulator of H2O2 concentration in the root meristem by directly
 regulating genes involved in oxidative stress response, such as PEROXIDASE
 28 (PER28). Moreover, we found that XAL1 is necessary for the H2O2-induced
 inhibition of primary root growth through the negative regulation of
 peroxidase and catalase activities. Furthermore, we found that XAL1, in
 conjunction with RETINOBLASTOMA-RELATED (RBR), is essential for positively
 regulating the differentiation of columella stem cells in response to
 moderate oxidative stress induced by H2O2 treatment.
description: Three biological replicates, each consisting of approximately 60
 plants, were prepared. The total RNA from 8dps roots was extracted using
 the Quick-RNA Miniprep Plus Kit (Zymo Research, Irvine, USA), including a
 DNaseI treatment step to remove contaminating DNA. The RNA integrity and
 quantity were assessed using a 2100 Bioanalyzer. Subsequently, the RNA was
 sequenced at the “Unidad de Síntesis y Secuenciación de DNA” of the
 Universidad Nacional Autónoma de México located at the Instituto de
 Biotecnología in Cuernavaca, Morelos, using an Illumina platform. For the
 analysis of differential transcript accumulation analysis, the raw
 sequencing data underwent trimming with Trimmomatic version 0.39 (Bolger
 <em>et al.</em>, 2014) using the following parameters:
 ILLUMINACLIP: 2:30:10 LEADING:3 TRAILING:3 SLIDING WINDOW:4:15 MINLEN:50
 HEADCROP:10. The quality of reads was evaluated with FastQC version 0.11.9
 (Andrews, 2010) both before and after the trimming process. Biological
 replicates were aligned to the Arabidopsis genome from TAIR10
 (https://www.arabidopsis.org/) and the abundance of the transcripts was
 estimated using Subread version 2.0.1 (Liao <em>et al.</em>,
 2019). Raw count tables were employed for differential transcript
 accumulation analysis using DESeq2 (Love <em>et al.</em>,
 2014). Differentially expressed genes (DEGs) were identified with an
 adjusted p-value (padj) &lt;0.05 and log2 fold change &gt; 1.5
 (Table S5). Gene Ontology (GO) enrichment analysis was conducted with
 agriGO v2.0 (http://systemsbiology.cau.edu.cn/agriGOv2/).
description: # Data for: Differentially expressed genes comparing WT plants vs xal1-2
 --- ## Description of the Data and file structure File
 name: Supplementary_data_DEGs_Zluhan-Martinez.xlsx Differentially
 expressed genes comparing WT plants vs xal1-2. The output of DESeq2 is
 shown. * Gene: gene locus * baseMean: mean value of normalized read counts
 of all the samples used for the comparison. * log2FoldChange: log2 values
 of fold changes of normalized read counts in datasets comparing WT and
 xal1-2. * lfcSE: the standard error estimate for the log2 fold change. *
 stat: Wald statistics. * pvalue: Wald test p-value. * padj:
 Benjamini-Hochberg adjusted p-value. * symbol: Gene name abbreviation. *
 Downregulated: if it is down- or up-regulated