Arabidopsis transcriptome dataset of the response of imbibed wild-type and glucosinolate-deficient seeds to nitrogen-containing compounds

Mailen Ortega-Cuadros; Sophie Aligon; Nubia Velasquez; Jerome Verdier; Philippe Grappin

doi:10.1016/j.dib.2023.109047

Arabidopsis transcriptome dataset of the response of imbibed wild-type and glucosinolate-deficient seeds to nitrogen-containing compounds

Data Brief. 2023 Mar 13:48:109047. doi: 10.1016/j.dib.2023.109047. eCollection 2023 Jun.

Authors

Mailen Ortega-Cuadros^{1

2}, Sophie Aligon¹, Nubia Velasquez¹, Jerome Verdier¹, Philippe Grappin¹

Affiliations

¹ Institut Agro, University Angers, INRAE, IRHS, SFR 4207 QuaSaV, Angers F-49000, France.
² Institute of Biology, University of Antioquia, Calle 67 N° 53-108, Medellín 050010, Colombia.

Abstract

The presented RNAseq data were obtained from Arabidopsis seeds dry and 6h imbibed to describe, in wild-type and glucosinolate (GSL)-deficient genotypes, the response at the RNA level to nitrogen compounds, i.e., potassium nitrate (KNO₃, 10mM), potassium thiocyanate (KSCN, 8µM). The cyp79B2 cyp79B3 (cyp79B2/B3) double mutant deficient in Indole GSL, the myb28 myb29 (myb28/29) double mutant deficient in aliphatic GSL, the quadruple mutant cyp79B2 cyp79B3 myb28 myb29 (qko) deficient in total GSL in the seed and the WT reference genotype in Col-0 background were used for the transcriptomic analysis. Total ARN was extracted using NucleoSpin® RNA Plant and Fungi kit. Library construction and sequencing were performed with DNBseq™ technology at Beijing Genomics Institute. FastQC was used to check reads quality and mapping analysis were made using a quasi-mapping alignment from Salmon. Gene expression changes in mutant seeds compared to WT were calculated using DESeq2 algorithms. This comparison with the qko, cyp79B2/B3 and myb28/29 mutants made it possible to identify 30220, 36885 and 23807 differentially expressed genes (DEGs), respectively. Mapping rate result was merge into a single report using MultiQC; graphic results were illustrated through Veen diagrams and volcano plots. Fastq raw data and count files from 45 samples are available in the repository Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) and can be consulted with the data identification number GSE221567 at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE221567.

Keywords: Arabidopsis; Glucosinolates; Potassium nitrate; Potassium thiocyanate; RNA-seq; Seed imbibition.