biostudies-arrayexpressCortijo SandraArabidopsis thalianahttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15039The aim of this dataset is to study inter-individual transcriptional variability in plants. Since it is associated with a paper studying the transcriptional variability for the nitrate transporter NRT2.1, the plants were grown on petri dishes with low nitrate (1mM KNO3). In total RNA-seq for 24 seedlings were done.biostudies-arrayexpressNucleic Acid Extraction - RNA was extracted from 11-day-old individual seedlings using the MagMAX™-96 Total RNA Isolation Kit (Ambion) following manufacturer’s instructions except for two changes: 60µl of Lysis/Binding solution were used instead of 100µl, and the elution was performed with 30µl of Elution Buffer instead of 50µl.Sample Collection - 11-day-old seedlings were harvested individually in liquid nitrogenGrowth Protocol - Col0 WT plants were grown on petri dishes after seed sterilisation and stratification, on a solid media containing 1mM KH2PO4, 1mM MgSO4, 0.25mM K2SO4, 0.25mM CaCl2, 0.1mM Na-Fe-EDTA, 2.5mM MES and microelements (50μM KCl, 30μM H3BO3, 5μM MnSO4, 1μM ZnSO4, 1μM CuSO4 and 0.1μM (NH4)6Mo7O24) and 1mM KNO3. A total of 4 plates per genotype and condition were prepared, with 30 seeds per plate (disposed over 2 rows). After 6 days of growth on long days at 22 degrees Celsius and a light intensity of 150 μmol m-2 s-1, seedlings that managed to do the heterotrophic-to-autotrophic transition and continued to grow were transferred to a new plate.Library Construction - Library for sequencing was performed by the novogene company on total RNA using a polyA enrichment method.Sequencing - Paired end 150bp illumina sequencing was performed by Novogene. When the number of reads obtained was lower than 20 million reads (for each pair) the sample was resequenced, explaining the double omount of FASTQ files for some samplesOrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - RNA quality and integrity were assessed using a Qubit™ Flex Fluorometer (Invitrogen). Generation of libraries and PE150 Illumina sequencing was performed by Novogene (Cambridge, UK) with approximately 20 million reads (of each end) per sample. Quality of reads was assessed using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/) and low quality reads were removed and trimmed using fastp (Chen, 2023). Mapping of the reads on the Arabidopsis thaliana genome (TAIR10) was performed with STAR (Dobin et al., 2013) and read count extracted thanks to htseq-count (Anders et al., 2015).UnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq 1000RNA-seq of coding RNAArabidopsis thalianaCortijo SandrafalseRNA-seq on single seedlings for 24 seedlings of Col0-WT grown with low nitrate on petri dishesThe aim of this dataset is to study inter-individual transcriptional variability in plants. Since it is associated with a paper studying the transcriptional variability for the nitrate transporter NRT2.1, the plants were grown on petri dishes with low nitrate (1mM KNO3). In total RNA-seq for 24 seedlings were done.2025-12-01T00:00:00Z2025-12-01T08:32:44.076Z2025-04-15T14:06:28.926ZE-MTAB-15039ERP171660EFO_0002944EFO_0004170EFO_0003789EFO_0005518EFO_0003816EFO_0003738EFO_0004184