{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Petros Sigalas"],"organism":["Triticum aestivum"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15558"],"description":["This dataset comprises RNA-seq data from whole root tissues of 12 A.E. Watkins wheat landraces that exhibit contrasting nitrogen (N) uptake and root proliferation traits, as identified through initial phenotypic screening. The selected landraces, along with the modern cultivar Paragon, were hydroponically grown under two nitrogen supply levels: High N (10 mM) and Low N (0.1 mM). The aim of the study was to identify genes and regulatory networks underlying the differential performance among the landraces and to compare their responses to N limitation."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - Plants were cultivated in a controlled environment chamber using the germination paper roll system (Bai et al., 2013; Zhu et al., 2005). A randomized block design was implemented, consisting of three blocks and two levels of nitrogen (N) supply: Low N (0.1 mM N) and High N (10 mM N), across 13 different genotypes (12 A.E. Watkins landraces + cv Paragon). Each replicate comprised two paper rolls with four seedlings. Growing conditions were set to a 16/8-hour light/dark cycle, with temperatures maintained at 20 °C during the day and 15 °C at night. Light intensity was maintained at 500 μmol m-2 s-1, with 70% relative humidity during the day and 80% during the night. The composition of the high N (10 mM N) solution was 1.5 mM Ca(NO3)2, 5 mM KNO3, 2 mM NaNO3, 1.5 mM MgSO4, 1 ","Nucleic Acid Extraction - Total RNA was extracted from approximately 500 mg of frozen tissue using a modified hot phenol extraction protocol (Verwoerd et al., 1989). To eliminate DNA contamination, DNase treatment was performed with RQ1 RNase-Free DNase (Promega), followed by additional purification using phenol/chloroform/isoamyl-alcohol extraction. The extracted total RNA was further purified using the RNeasy MinElute Cleanup system (Qiagen). RNA integrity and purity were assessed via gel electrophoresis and spectrophotometric analysis using the Nanodrop Spectrophotometer 2000c (Thermo Scientific).","Sequencing - Sequencing was performed by the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics, Oxford University. Libraries underwent multiplexing and were loaded onto flow cells. Next-generation sequencing was performed on the Illumina HiSeq 4000 platform, using a 2x150 bp pair-end configuration. Raw paired-end data were delivered in fastq format.","Sample Collection - The entire root system of plants was harvested 11 days after introduction to the growing system. Samples were rapidly frozen in liquid nitrogen and stored at -80 °C until processing. Tissue samples from 8 plants were pooled per biological replicate.","Library Construction - Quality control, poly-A selection for rRNA removal, library preparation, and multiplexing were performed by the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics, Oxford University, according to their established standard procedures. RNA library preparation utilized the Illumina TruSeq Stranded mRNA kit."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Raw sequencing reads were pre-processed using Trimmomatic v0.36 (Bolger et al., 2014) to remove adapter sequences. Reads shorter than 100 bases following adapter removal were discarded. The resulting trimmed reads were pseudo-aligned to the wheat pan-transcriptome published by Coombes et al. (2024) using kallisto v0.46.0.4 (Bray et al., 2016) to estimate transcript abundances, reported as transcripts per million (TPM).","Data Transformation - Gene-level abundance matrices were generated from transcript-level quantifications using the tximport package (v1.24.0; Soneson et al., 2015), in combination with a custom tx2gene mapping file that links pan-transcriptome transcripts to corresponding CS reference genes."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 4000"],"study_type":["RNA-seq of coding RNA"],"species":["Triticum aestivum"],"pubmed_authors":["Malcolm Hawkesford","Peter Buchner","Petros Sigalas"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptomic analysis in root tissue of 12 wheat A.E. Watkins landraces with contrasting root proliferation and nitrogen uptake grown under two nitrogen levels","description":"This dataset comprises RNA-seq data from whole root tissues of 12 A.E. Watkins wheat landraces that exhibit contrasting nitrogen (N) uptake and root proliferation traits, as identified through initial phenotypic screening. The selected landraces, along with the modern cultivar Paragon, were hydroponically grown under two nitrogen supply levels: High N (10 mM) and Low N (0.1 mM). The aim of the study was to identify genes and regulatory networks underlying the differential performance among the landraces and to compare their responses to N limitation.","dates":{"release":"2026-08-28T00:00:00Z","modification":"2026-08-28T01:00:48.346Z","creation":"2025-09-05T14:42:39.11Z"},"accession":"E-MTAB-15558","cross_references":{"ENA":["ERP179693"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}