Ortega-Cuadros Mailen, Aligon Sophie, Velasquez Nubia, Verdier Jerome, Grappin Philippe
Institut Agro, University Angers, INRAE, IRHS, SFR 4207 QuaSaV, Angers F-49000, France.
Institute of Biology, University of Antioquia, Calle 67 N° 53-108, Medellín 050010, Colombia.
Data Brief. 2023 Mar 13;48:109047. doi: 10.1016/j.dib.2023.109047. eCollection 2023 Jun.
The presented RNAseq data were obtained from seeds dry and 6h imbibed to describe, in wild-type and glucosinolate (GSL)-deficient genotypes, the response at the RNA level to nitrogen compounds, ., potassium nitrate (KNO, 10mM), potassium thiocyanate (KSCN, 8µM). The double mutant deficient in Indole GSL, the double mutant deficient in aliphatic GSL, the quadruple mutant 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 and 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.
所呈现的RNA测序数据取自干燥种子和吸水6小时的种子，以描述野生型和缺乏硫代葡萄糖苷（GSL）的基因型在RNA水平上对氮化合物（即硝酸钾（KNO₃，10mM）、硫氰酸钾（KSCN，8µM））的反应。吲哚GSL缺陷型双突变体、脂肪族GSL缺陷型双突变体、种子中总GSL缺陷型四突变体以及Col-0背景下的野生型参考基因型用于转录组分析。使用NucleoSpin® RNA Plant and Fungi试剂盒提取总RNA。在北京基因组研究所采用DNBseq™技术进行文库构建和测序。使用FastQC检查读段质量，并使用Salmon的准映射比对进行映射分析。使用DESeq2算法计算突变种子与野生型相比的基因表达变化。与[具体双突变体]和[具体双突变体]的比较分别鉴定出30220、36885和23807个差异表达基因（DEG）。使用MultiQC将映射率结果合并到一份报告中；通过维恩图和火山图展示图形结果。来自45个样本的Fastq原始数据和计数文件可在国家生物技术信息中心（NCBI）的序列读取存档库（SRA）中获取，可通过数据识别号GSE221567在https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE221567进行查询。
