{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Steven Maere"],"organism":["Zea mays"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14898"],"description":["A thorough understanding of spatiotemporal gene expression during organ development and in response to stress is essential for targeted improvement of crops such as maize. In this study, several developmental zones of the ear and of leaves and internodes of different ranks were transcriptome-profiled in the stiff-stalk Zea mays L. inbred line B104 at different growth stages under both well-watered and drought conditions, resulting in a high-resolution spatiotemporal gene expression atlas. This atlas and the associated phenotypic data offer a deeper understanding of the similarities and differences among maize shoot organs and tissues during development and in response to drought, providing a valuable resource for engineering organ-specific traits in maize."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - For all experiments, the stiff-stalk maize (Zea mays L.) inbred line B104 was grown on the Phenovision plant phenotyping platform (semi-controlled greenhouse setting) at the VIB-UGent Center for Plant Systems Biology in Ghent, Belgium (see Verbraeken et al. (2021) Plant Phys 186: 1336–1353, doi:10.1093/plphys/kiab155 for Phenovision details). Three biological repeats of the entire spatiotemporal transcriptome profiling experiment were performed on this platform in September–November 2015 (batch B1), March-May 2016 (B2) and September–November 2016 (B3). Plants were sown individually in 7-l pots with approximately 850 g (dry weight) of peat-based soil enriched with osmocote slow-release fertilizer (N.V. Van Israel, Belgium).  The plants were grown under well-watered (Control) conditions or subjected to drought treatment starting at either the V5-stage (V5-drought) or the V12-stage (V12-drought). Plants were automatically watered each day, receiving water up to a specified gravimetric soil water content. The target soil water contents were 2.4 g water*g-1 dry soil for the Control treatment, at a soil water potential of around -10 kPa, which is close to field capacity, and 1.4 g water*g-1 dry soil for V5-Drought and V12-Drought treatments, corresponding to a soil water potential of around -100 kPa. All drought-treated pots started at the well-watered target soil water content and were switched to drought conditions at either the V5-stage (vegetative stage drought) or the V12-stage (reproductive stage drought). It took several days for the soil to dry down below the target soil water content and for the pots to receive daily watering again.","Library Construction - The extracted RNA was sent to GATC Biotech AG (Constance, Germany) for library construction and RNA sequencing. The libraries were constructed using NEBNext Kit for Illumina with poly-A selection.","Nucleic Acid Extraction - Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions, followed by DNase treatment using the RQ1 RNase-free DNase kit (Promega).","Sequencing - The mRNA-enriched libraries were sequenced in a paired-end mode with a read length of 125 bp on an Illumina HiSeq4000 with the TruSeq SBS Kit v3 (Illumina).","Sample Collection - For each of the treatments (well-watered, V5 drought and V12 drought), different zones of leaf, internode and ear were sampled for RNA sequencing at distinct time points. For leaf sampling, the whole leaf was sampled before leaf emergence from the whorl. After the emergence, different leaf zones were sampled, as identified according to the physiological characteristics of the leaf. In brief, the division zone was sampled between 15-25 mm from the leaf base and contained mostly dividing cells. The elongation zone was sampled between 50-60 mm from the leaf base and contained mostly growing cells. The differentiation zone was sampled between 100-140 mm from the leaf base and contained cells that stopped elongation but were not fully photosynthetically active. The mature zone was sampled as a piece of 40 mm in length at approximately the middle of the emerged leaf blade where cells were fully developed. During the vegetative stage (from V5 to 8 days after L18 appearance), L9, L12, L15 and L18 were sampled, while during the reproductive stage (from 4 days before ear appearance to silk emergence), the mature zone of L12, L18 and the ear leaf (usually L14 or L15) were sampled. Internodes were sampled in their entirety at the earliest growth stages. In the later stages, they were divided lengthwise in the middle, into a low (basal) and high (apical) zone or separated into three zones, with middle zone. The Int9, Int12 and Int15 were sampled during the vegetative stage while the ear internode was sampled during the reproductive stage. Similar to the internode, the ears were sampled either in their entirety, divided lengthwise into two equally long parts or divided lengthwise into three equally long parts. In total, 272 biological materials were collected for transcriptome analysis. For each of them, three biological replicates from independent greenhouse experiments were examined and each was a pool of three randomly chosen plants. Only for six materials, there were only two biological replicates (Earx0_IntEarMid_V12, L18x0_IntEar_C, L18x0_IntEar_V5, L18x4_IntEarHigh_C, Silk_IntEarLow_V5, L9x0_L9Elong_V5)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Count data were filtered to remove remove 3291 genes with zero counts across all samples and 7690 further genes that have cpm (counts per million) values > 0.5 in less than three samples, resulting in a filtered count matrix with 28342 genes. This filtered matrix was normalized and transformed using the (vst() function of the DESeq2 R package, which performs DESeq2 size factor calculation, normalization for library size and fast estimation of the mean-dispersion trend in the data followed by a variance stabilizing transformation (vst, Love et al. (2014)Genome Biol 15, 550, https://doi.org/10.1186/s13059-014-0550-8).","Sequence Alignment - The quality of the raw data was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, version 0.11.5). Quality filtering was then performed with Trimmomatic (version 0.32) to remove adapters and low-quality reads. The filtered reads were subsequently mapped to the maize B73 reference genome sequence V3 (http://ftp.maizesequence.org/B73_RefGen_v3/) using GSNAP (v2013-06-27). Concordantly paired reads that uniquely map to the genome were used for quantification on gene level with htseq-count from the HTSeq.py python package (version 0.6.1p1). All analyses were done on the Galaxy instance of the VIB-UGent Center for Plant Systems Biology."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 4000"],"study_type":["RNA-seq of coding RNA"],"species":["Zea mays"],"pubmed_authors":["Steven Maere"],"additional_accession":[]},"is_claimable":false,"name":"High-resolution transcriptional atlas of growing maize shoot organs throughout plant development under well-watered and drought conditions","description":"A thorough understanding of spatiotemporal gene expression during organ development and in response to stress is essential for targeted improvement of crops such as maize. In this study, several developmental zones of the ear and of leaves and internodes of different ranks were transcriptome-profiled in the stiff-stalk Zea mays L. inbred line B104 at different growth stages under both well-watered and drought conditions, resulting in a high-resolution spatiotemporal gene expression atlas. This atlas and the associated phenotypic data offer a deeper understanding of the similarities and differences among maize shoot organs and tissues during development and in response to drought, providing a valuable resource for engineering organ-specific traits in maize.","dates":{"release":"2026-03-05T00:00:00Z","modification":"2026-03-05T13:57:48.15Z","creation":"2025-02-28T12:04:06.77Z"},"accession":"E-MTAB-14898","cross_references":{"ENA":["ERP169752"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}