biostudies-arrayexpressPetros SigalasTriticum aestivumhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15529The aim of this study was to investigate transcriptional changes underlying the zinc (Zn) deficiency response in root and shoot tissues of bread wheat. Triticum aestivum cv. Paragon seedlings were hydroponically grown and subjected to Zn starvation (0 μM ZnCl₂) starting at 14 days after germination. Samples were collected at 1, 3, 5, and 7 days following Zn withdrawal. RNA-seq was performed on whole root and shoot tissues, with three biological replicates per treatment and time point. Control plants supplied with 8 μM ZnCl₂ were included to distinguish Zn deficiency transcriptional responses.biostudies-arrayexpressGrowth Protocol - Triticum aestivum (cv. Paragon) seedlings were hydroponically grown in a controlled environment chamber using a custom-built aerated hydroponic system. Each seedling was cultivated individually in 1 L culture pots. Growth conditions were maintained at 20 °C during the day and 16 °C at night, with a 16-hour photoperiod. Light was provided by fluorescent bulbs at an intensity of 500 μmol m⁻² s⁻¹. Relative humidity was maintained at 70% during the day and 80% at night. The composition of the nutrient solution was 1.5 mM Ca(NO₃)₂, 5 mM KNO₃, 2 mM NaNO₃, 1 mM MgSO₄, 0.5 mM KH₂PO₄, 25 μM FeNaEDTA, 0.2 μM CuCl₂, 1 μM H₃BO₃, 0.6 μM MnCl₂, 0.1 μM Na₂MoO₄, 5 μM KCl, 8 μM ZnCl₂, including the chelator 75.5 μM HEDTA. For zinc-deficiency treatments, ZnCl₂ was omitted (0 μM). 2.35 mM MES monohydrate was added as buffer, and the pH was adjusted to 5.8 using KOH. The nutrient solution was changed three times a week. Seedlings were transferred to the hydroponic system 7 days after germination. For the first 3 days, plants received half-strength nutrient solution, followed by full-strength solution. Zinc-starvation treatment began at 14 days after germination, when plants were supplied with nutrient solution lacking ZnCl₂.Sample Collection - Samples were collected at 1, 3, 5, and 7 days after zinc starvation. At each time point, plants were separated into root and shoot tissues. Roots were rinsed three times with deionised water and briefly dried on paper towels. Whole root and shoot samples were immediately frozen in liquid nitrogen and stored at −80 °C until RNA extraction.Sequencing - Sequencing was performed by Novogene UK. Quantified libraries were prepared using the Novogene NGS RNA Library Prep Set (PT042), pooled, and loaded onto a flow cell. Next-generation sequencing was carried out on the Illumina NovaSeq 6000 platform using a 2 × 150 bp paired-end configuration. Raw paired-end reads were delivered in FASTQ format following de-multiplexing and standard adapter trimming by the sequencing provider.Library Construction - Library preparation, poly-A selection for rRNA removal, quality control, and multiplexing were performed by Novogene UK following their standard RNA-seq workflow. After fragmentation, first-strand cDNA synthesis was carried out using random hexamer primers, followed by second-strand synthesis using dTTP (for non-directional libraries). Subsequently, end repair, A-tailing, adapter ligation, size selection, PCR amplification, and purification were performed. Library quality was assessed using Qubit fluorometry and qPCR quantification, and size distribution was evaluated using a fragment analyser.Nucleic Acid Extraction - Samples were ground to a fine powder using either a pestle and mortar in liquid nitrogen or a freezer mill (SPEX SamplePrep 6870), depending on sample quantity. Total RNA was extracted from approximately 1 g of ground tissue using a modified protocol based on Verwoerd et al. (1989), as described in Evens et al. (2017). To ensure no DNA carryover, DNase treatment was performed using RQ1 RNase-Free DNase (Promega). After DNase treatment, RNA was further purified by phenol/chloroform/isoamyl-alcohol purification. Prior to RNA sequencing, total RNA was further purified using the GeneJET RNA Cleanup and Concentration Micro Kit (Thermo Scientific), following the manufacturer’s protocol. RNA concentration was determined using the Qubit Broad Range Assay (Invitrogen), and purity was assessed via A260/A280 ratio using a NanoDrop 2000 spectrophotometer (Thermo Scientific). RNA integrity was also evaluated by electrophoresis of 500 ng RNA on a 1% agarose TAE gel.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Quality control of the raw sequencing reads was performed using FastQC tool. Adapter contamination was minimal, and trimming was therefore omitted, following the recommendations of Liao and Shi (2020). Raw reads were pseudo-aligned to IWGSC RefSeq v1.0 annotation v1.1 using Kallisto v0.46.0.4 (Bray et al., 2016). The package tximport v1.24.0 was used to create gene-level abundance from the transcript abundances (Soneson et al., 2015)Data Transformation - The Kallisto tool used for pseudo-alignment directly reports transcript abundance as Transcripts Per Million (TPM) values. The package tximport v1.24.0 was used to create gene-level abundance from the transcript abundances (Soneson et al., 2015).MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNATriticum aestivumNick EvensMalcolm HawkesfordPetros SigalasfalseTime-course RNA-seq analysis in root and shoot tissues of zinc-deficient Triticum aestivum cv. Paragon (bread wheat)The aim of this study was to investigate transcriptional changes underlying the zinc (Zn) deficiency response in root and shoot tissues of bread wheat. Triticum aestivum cv. Paragon seedlings were hydroponically grown and subjected to Zn starvation (0 μM ZnCl₂) starting at 14 days after germination. Samples were collected at 1, 3, 5, and 7 days following Zn withdrawal. RNA-seq was performed on whole root and shoot tissues, with three biological replicates per treatment and time point. Control plants supplied with 8 μM ZnCl₂ were included to distinguish Zn deficiency transcriptional responses.2026-08-24T00:00:00Z2026-08-24T01:00:50.481Z2025-09-02T20:40:04.488ZE-MTAB-15529ERP179527EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184