Study Identified Summary of study Brief SRA description Manuscript title
Azhurnaya development Developmental time-course of Azhurnaya 70 tissue/timepoints from Azhurnaya developmental stages The transcriptional landscape of polyploid wheat
PAMP PAMP innoculation of seedlings Leaves innoculated with flg22, chitin and water to study PAMP responses The transcriptional landscape of polyploid wheat
spike drought Spikes with water stress Water stress was applied to a double haploid population at early booting. RNA was sequenced from spikes. The transcriptional landscape of polyploid wheat
CS seedlings spike Chinese Spring seedling (leaves and roots) and spikes at anthesis Seedlings of Chinese Spring were divided into leaves and roots, and spikes were collected at anthesis. The transcriptional landscape of polyploid wheat
CS vegetative Chinese Spring leaves and roots from seven leaf stage Vegetative (seven leaf stage) roots and leaves were harvested from Chinese Spring. The transcriptional landscape of polyploid wheat
phosphate Phosphate starvation in roots and shoots Transcriptome profiles of wheat variety Chinese Spring (CS) in response to Pi starvation (−P) for 10 days. Characterisation of the wheat (Triticum aestivum L.) transcriptome by de novo assembly for the discovery of phosphate starvation-responsive genes: gene expression in Pi-stressed wheat
CS grain Grain tissue-specific developmental timecourse Analysis of the cell type specific expression of homeologous genes in the developing wheat grain Genome interplay in the grain transcriptome of hexaploid bread wheat
12dpa grain Grain tissue-specific expression at 12 days post anthesis Inner pericarp, outer pericarp and endosperm layers from developing grain of bread wheat cv. Holdfast at 12 days post-anthesis. Heterologous expression and transcript analysis of gibberellin biosynthetic genes of grasses reveals novel functionality in the GA3ox family
flag leaf Flag leaf downregulation of GPC Wild type bread wheat plants and GPC RNAi plants 12 days after anthesis Effect of the down-regulation of the high Grain Protein Content (GPC) genes on the wheat transcriptome during monocarpic senescence
grain dissection Grain tissue-specific developmental timecourse Transcriptomes of the aleurone and starchy endosperm tissues of the wheat seed (Triticum aestivum) at time points critical to the development of the aleurone layer of 6, 9 and 14 days post anthesis. Gene expression in the developing aleurone and starchy endosperm of wheat
stripe rust Stripe rust infected seedlings Pool of stripe rust infected wheat leaves Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors
septoria Septoria tritici infected seedlings Molecular mechanisms underlying the interplay between fungal pathogenicity and host responses at specific growth phases and the factors triggering disease transition. Transcriptional Reprogramming of Wheat and the Hemibiotrophic Pathogen Septoria tritici during Two Phases of the Compatible Interaction
fusarium 30 50h Fusarium head blight infected spikelets Near isogenic wheat lines, differing in the presence of the Fusarium graminearum FHB-resistance QTL Fhb1 and Qfhs.ifa-5A, under disease pressure (30 and 50 hai) as well as with mock-inoculation Quantitative trait loci-dependent analysis of a gene co-expression network associated with Fusarium head blight resistance in bread wheat (Triticum aestivum L.)
nullitetra Shoots and leaves of nulli tetra group 1 and group 5 RNAseq of nulli-tetrasomic wheat lines (shoots and leaves) Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat
early grain Grain tissue-specific developmental timecourse Gene expression profiling of morphological stage of developing wheat grain Evaluation of Assembly Strategies Using RNA-Seq Data Associated with Grain Development of Wheat (Triticum aestivum L.)
stamen pistil Comparison of stamen, pistil and pistilloidy expression Transcriptional profiling of pistillody stamen, pistil and stamen in wheat line HTS-1 Pistillody mutant reveals key insights into stamen and pistil development in wheat (Triticum aestivum L.)
stripe rust powdery mildew Stripe rust and powdery mildew timecourse of infection in seedlings Transcriptome Divergence and Overlap for Wheat in Response to Stripe rust and Powdery Mildew Pathogen Stress Large-scale transcriptome comparison reveals distinct gene activations in wheat responding to stripe rust and powdery mildew.
drought heat Drought and heat stress time-course in seedlings RNAseq of 1-week old wheat seedling leaves subjected to drought stress, heat stress and their combination before (0h) and after stress (1h or 6h) Temporal transcriptome profiling reveals expression partitioning of homeologous genes contributing to heat and drought acclimation in wheat (Triticum aestivum L.)
4A dormancy Grain developmental timecourse with 4A dormancy QTL This study was to identify candidate genes underlying the 4AL QTL for grain dormancy in wheat. RNA was sequenced from pooled NILs segregating for the QTL Transcriptomic analysis of wheat near-isogenic lines identifies PM19-A1 and A2 as candidates for a major dormancy QTL
CS development Developmental time-course of Chinese Spring Whole transcriptome sequencing of wheat 3B chromosome Structural and functional partitioning of bread wheat chromosome 3B
CS 6 tissues Six unreplicated tissues from Chinese Spring. Seedlings, roots, leaves, stem, spike and grain from Chinese Spring An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations
fusarium 0h to 48h Timecourse of spikelets inoculated with fusarium head blight Spikes from NILs for Fhb1 were inoculated with Fusarium graminearum. They were sequenced from 0 to 48 h post innoculation. Suppressed recombination and unique candidate genes in the divergent haplotype encoding Fhb1, a major Fusarium head blight resistance locus in wheat
crown rot Coleoptile infection with Fusarium pseudograminearum (crown rot) Coleoptiles inoculated with Fusarium pseudograminearum, mock and treatment were sequenced 3 days post infection. The Fusarium crown rot pathogen Fusarium pseudograminearum triggers a suite of transcriptional and metabolic changes in bread wheat (Triticum aestivum L.)
magnaporthe Leaves naturally infected with Magnaporthe oryzae Symptomatic (Magnaporthe oryzae) and nonsymptomatic leaves were sequenced from Bangladesh. Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae
PEG Seedlings with PEG to simulate drought Seedlings had PEG 6000 applied from 2 to 12 hours. N/A
fusarium hormones spikes innoculated with fusarium head blight and ABA/GA Spikes were inoculated with Fusarium graminearum and ABA or GA. Exogenous Abscisic Acid and Gibberellic Acid Elicit Opposing Effects on Fusarium graminearum Infection in Wheat
CS flag leaf Chinese Spring flag leaves, 6 timepoints Chinese Spring flag leaves harvested from ear emergence to 30 days post anthesis. N/A
microspores Microspores in tissue culture and cold Microspores were harvested after tissue culture and cold treatment. Analysis of wheat microspore embryogenesis induction by transcriptome and small RNA sequencing using the highly responsive cultivar “Svilena”
septoria 2 Zymoseptoria tritici infected seedlings Riband seedlings infected with Zymoseptoria tritici. Transcriptome and Metabolite Profiling of the Infection Cycle of Zymoseptoria tritici on Wheat Reveals a Biphasic Interaction with Plant Immunity Involving Differential Pathogen Chromosomal Contributions and a Variation on the Hemibiotrophic Lifestyle Definition
CS fusarium CS spikes inoculated with fusarium head blight CS spikes innoculated with Fusarium graminearum. Development and Validation of Thinopyrum elongatum–Expressed Molecular Markers Specific for the Long Arm of Chromosome 7E
crown rot 2 Shoots from NILs segregating for crown rot resistance Shoots from NILs segregating for resistance to Fusarium pseudograminearum. Inoculated and mock samples. Transcriptome and Allele Specificity Associated with a 3BL Locus for Fusarium Crown Rot Resistance in Bread Wheat
cold Shoots after 2 weeks cold Shoots after 2 weeks cold to examine cold-induced lipid pathways. Understanding the Biochemical Basis of Temperature-Induced Lipid Pathway Adjustments in Plants
stripe rust 2 Stripe rust infected seedlings Timecourse of Vuka and Avocet+Yr5 innoculated with stripe rust. The host-pathogen interaction between wheat and yellow rust induces temporally coordinated waves of gene expression
synthetic Developmental time-course of synthetic hexaploid RNAseq of three tissues of nascent allohexaploid wheat and its following generations, their progenitors, and Chinese Spring mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in Nascent Hexaploid Wheat
flag leaf senescence Gene expression during a timecourse of flag leaf senescence Triticum aestivum flag leaf senescence Identification of transcription factors regulating senescence in wheat through gene regulatory network modelling
CS meiosis Chinese Spring early meiosis, early prophase Transcriptome analysis of early meiosis in wheat in the presence and absence of the Ph1 locus Genome-wide transcription during early wheat meiosis is independent of synapsis, ploidy level and the Ph1 locus


If you use expVIP please cite the following papers:

Ricardo Ramirez-Gonzalez, Philippa Borrill et al. The transcriptional landscape of hexaploid wheat across tissues and cultivars Science 2018: Vol. 361, Issue 6403, eaar6089. doi:10.1126/science.aar6089

Free access
Philippa Borrill, Ricardo Ramirez-Gonzalez, and Cristobal Uauy expVIP: a customisable RNA-seq data analysis and visualisation platform Plant Physiology 2016 : pp.15.01667v1-pp.01667.2015. doi:10.1104/pp.15.01667


expVIP was developed by Ricardo H. Ramirez-Gonzalez(github) and Bijan Ghasemi Afshar (github) within the Uauy lab.