biostudies-arrayexpressUnknownTranscriptomicsGenomicsProteomicsRichard ClarkRNA-seq of coding RNAHordeum vulgareHordeum vulgarehttps://www.ebi.ac.uk/biostudies/studies/E-GEOD-83676Spider mites, including the two-spotted spider mite (Tetranychus urticae, TSSM) and the Banks grass mite (Oligonychus pratensis, BGM), are becoming increasingly important agricultural pests. The TSSM is an extreme generalist documented to feed on more than 1100 plant hosts. In contrast, the BGM is a grass specialist, with hosts including important cereal crops like maize, wheat, sorghum and barley. Historically, studies of plant-herbivore interactions have focused largely on insects. However, far less is known about plant responses to spider mite herbivores, especially in grasses, and whether responses differ between generalists and specialists. To identify plant defense pathways responding to spider mites, we collected time course RNA-seq data from barley (Hordeum vulgare L.) infested with TSSMs and BGMs. Additionally, and as a comparison to the physical damage caused by spider mite feeding, a wounding treatment was also included. The experiment was performed with four biological replicates across each of the following (28 samples in total): no infestation (C, control), 2hr after wounding (W2), 24hr after wounding (W24), 2hr after TSSM infestation (T2), 24hr after TSSM infestation (T24), 2hr after BGM infestation (B2), and 24hr after BGM infestation (B24).biostudies-arrayexpressLibrary Construction - Leaf tissue was ground to fine powder in liquid nitrogen. Total RNA was prepared using the DirectZol RNA extraction kit (Zymo Research). Quality of the RNA extractions was assessed using a Bioanalyzer (Aligent). The libraries were prepared at the University of Utah High Throughput Genomics facility using the Illumina TruSeq Stranded mRNA Library Preparation Kit with poly(A) selection.Growth Protocol - The barley (Hordeum vulgare, Morex variety) plants used for the experiments were germinated and grown in a growth chamber with 16h-light/8h-dark photoperiod at a temperature of approximately 20 degrees C. They were cultivated using Sun Gro® Metro-Mix® 900 Grower Mix, watered as needed, and fertilized weekly with 200ppm NutriCulture 18N-6P-18K.Sample Treatment - The 5th leaves of 30-day-old barley plants were used for the experiment. Mite movement was restrained by barriers made of a non-toxic wax (TangleFoot). Mites were allowed to feed on both sides of a leaf section defined by TangleFoot barriers. The barley leaf sections were infested with healthy adult females, 400 mites per leaf section for 2hr-timepoints and 200 mites per leaf section for 24hr-timepoints. Wounding treatment was applied by rubbing 60 grit sand paper on both sides of the leaf. The control leaves received the TangleFoot barriers but none of the treatments. Mite infestation and wounding treatments were applied at 24hr and 2hr before sample collection. All samples were collected at the same time to limit the effects of the circadian cycle and any minor environmental differences on gene expression.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesRichard ClarkAlice RuckertHuyen BuiRobert GreenhalghRicardo RamirezData Transformation - Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCS v2.2.38 and RTA v1.18.61), a 125 cycle paired-end sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4003), and the resulting reads were aligned to the H. vulgare reference genome (082214) with STAR 2.5.1b in two-pass alignment mode (alignments were independent of the existing reference annotation). Read counts for genes in the ASM32608v1 annotation were obtained using HTSeq 0.6.0 with --stranded reverse and --feature transcript. Genome_build: 082214 (genome sequence) and ASM32608v1 (genome annotation) were downloaded from the barley genome site at ensembl.org. Supplementary_files_format_and_content: Tab-delimited text file with counts of reads per gene from alignments as assessed with HTSeq (expression across all samples is included in the single processed data file).falseTime course RNA-seq data from barley infested with Tetranychus urticae and Banks grass miteSpider mites, including the two-spotted spider mite (Tetranychus urticae, TSSM) and the Banks grass mite (Oligonychus pratensis, BGM), are becoming increasingly important agricultural pests. The TSSM is an extreme generalist documented to feed on more than 1100 plant hosts. In contrast, the BGM is a grass specialist, with hosts including important cereal crops like maize, wheat, sorghum and barley. Historically, studies of plant-herbivore interactions have focused largely on insects. However, far less is known about plant responses to spider mite herbivores, especially in grasses, and whether responses differ between generalists and specialists. To identify plant defense pathways responding to spider mites, we collected time course RNA-seq data from barley (Hordeum vulgare L.) infested with TSSMs and BGMs. Additionally, and as a comparison to the physical damage caused by spider mite feeding, a wounding treatment was also included. The experiment was performed with four biological replicates across each of the following (28 samples in total): no infestation (C, control), 2hr after wounding (W2), 24hr after wounding (W24), 2hr after TSSM infestation (T2), 24hr after TSSM infestation (T24), 2hr after BGM infestation (B2), and 24hr after BGM infestation (B24).2016-06-24T00:00:00Z2023-09-22T15:44:08.377Z2022-03-10T08:51:36.211ZE-GEOD-83676SRP077020EFO_0003738