RNA-seq of soybean (Glycine max cv. Daewonkong) under Salinity stress and normal conditions
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina NovaSeq 6000
ORGANISM(S): Glycine max
SUBMITTER: Doheon Choi
PROVIDER: E-MTAB-17141 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We collected the samples, rice anthers at the anthesis stage from the wild type and paspro1/paspro2 mutant anther (Dongjin cultivar), from our field and immediately froze the samples with liquid nitrogen. Later, We extract RNA from the samples and performed RNA sequencing.
2023-12-31 | E-MTAB-12375 | biostudies-arrayexpress
Project description:Two Arabidopsis thaliana splicing factor [AtU2AF65 isoforms (AtU2AF65a and AtU2AF65b)] mutants displayed the opposite flowering phenotypes. To assay the RNA processing including alternative splicing and pre-mRNA splicing of target genes of this protein in Arabidopsis, the 7-day seedlings (shoot apices) of wild type atu2af65a and atu2af65b mutants were used for RNA-Seq.
2023-05-01 | E-MTAB-12648 | biostudies-arrayexpress
Project description:In this study a gene expression (i.e., RNAseq) analysis was performed in HEK293T-ACE2 cellular model upon infection with viral particle belonging to VOC Delta (MOI: 0.026) for 24 hours in order to have a global picture of the transcriptome landscape in response to early phase of infection of SARS-CoV-2 ( VOC Delta infection and to evaluate the role of Ca2+ in HEK293-ACE2 cellular model and transfer to homeostasis in SARS-COV-2 patients (by Pasqualino de Antonellis1-2* and Veronica Ferrucci 1-2* (first authors) et al. and Massimo Zollo1-2# (corresponding author). Manuscript in preparation 2022 July 15th 2022. Short title "ATP2B1 (PMCA1), regulated by FOXO3, influences susceptibility to severe COVID19".
2022-12-01 | E-MTAB-11973 | biostudies-arrayexpress
Project description:Senegalese sole males born and raised in captivity (F1 males) do not spawn naturally and typically display lower gamete quality when compared with wild individuals. Broodstock nutrition is an important aspect when dealing with reproduction because it influences not only fish health, but also gamete and progeny quality. The usage of dietary algae antioxidants to improve fish reproduction is under-explored, especially in terms of the male reproductive system. In this experiment, 6 % of a blended meal of Phaeodactylum tricornutum and Gracilaria gracilis was incorporated in Senegalese sole broodstock feed, to evaluate the effects on sperm quality of F1 males throughout the breeding season. RNA-seq was employed to assess differences in the gonadal tissue of fish fed the algae supplemented diets.
2024-08-01 | E-MTAB-14218 | biostudies-arrayexpress
Project description:Fish in aquaculture farms frequently face unfavarouble husbandry conditions and other unpredictable situations, which are sometimes part of routine procedures. However, managing stress originated from these situations is crucial to ensure the sustainability of the production. When fish is exposed to prolonged stress, and overload of the physiological systems can occur and the fish may no longer be able to adapt and restore homeostasis, and this can impair the animal performance, such as growth and immunity, and consequently fish welfare. In this study the genes and gene families responsible for the molecular stress response to different challenges in gilthead seabream was assessed. Gilthead seabream adults were exposed to overcrowding, net-handling and hypoxia, in separate trials, each against a control group. Overcrowding and net-handling trials lasted for a month and half (chronic stress) and hypoxia for 48h (acute stress). The liver was the chosen organ for this transcriptomics analysis as this plays a crucial role in stress adaptation. The characterization of stress adaptation mechanisms provides valuable knowledge for the future selective breeding of more resilient commercial species that can thrive under changing conditions and adapt well to life in captivity, while ensuring high welfare standards.
2023-04-30 | E-MTAB-12842 | biostudies-arrayexpress
Project description:Various rice tissues were collected and immediately frozen from Dongin cultivar (Oryza sativa L. japonica).
2022-12-31 | E-MTAB-11005 | biostudies-arrayexpress
Project description:Abiotic stresses such as salinity are very important factors limiting rice growth and productivity around the world. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice responsive to salinity stress, try to elucidate the difference of genome-wide gene expression profiling of two contrasting rice genotypes in response to salt stress and to discover the salinity related genes and gene interaction and networks. Under salinity condition, the number of differentially expressed genes (DEGs) in 177-103 was more than that in IR64, and most of up-regulated DEGs in 177-103 are response to stress. But in IR64, most of up-regulated DEGs are transcription related genes. The DEGs under salinity showed very strong tissue specificity, the number of DEGs in leaf was more than that in root. A lot of genes differentially expressed by exogenous ABA treatment under salinity condition, such as Leaf senescence protein, 1-deoxy-D-xylulose 5-phosphate synthase 2 precursor and Protein of unknown function DUF26 were induced by ABA and contributed to salinity tolerance. In this study, the gene expression patterns across two organs including leaves and roots at seedling stage were characterized under control, salinity, salinity+ABA treatments by using the Affymetrix rice microarray platform based on a salinity tolerant rice line derived from IR64.
2015-11-02 | E-GEOD-58603 | biostudies-arrayexpress
Project description:With the growing limitations on arable land, alfalfa (a widely cultivated, low-input forage) is now being selected to extend cultivation into saline lands for low-cost biofeedstock purposes. Here, minerals and transcriptome profiles were compared between two new salinity-tolerant North American alfalfa breeding populations and a more salinity-sensitive Western Canadian alfalfa population grown under hydroponic saline conditions. All three populations accumulated two-fold higher sodium in roots than shoots as a function of increased electrical conductivity. At least 50% of differentially expressed genes (p < 0.05) were down-regulated in the salt-sensitive population growing under high salinity, while remaining unchanged in the saline-tolerant populations. In particular, most reduction in transcript levels in the salt-sensitive population were observed in genes specifying cell wall structural components, lipids, secondary metabolism, auxin and ethylene hormones, development, transport, signalling, heat shock, proteolysis, pathogenesis-response, abiotic stress, RNA processing, and protein metabolism. Transcript diversity for transcription factors, protein modification, and protein degradation genes was also more strongly affected in salt-tolerant CW064027 than in salt-tolerant Bridgeview and salt-sensitive Rangelander, while both saline-tolerant populations showed more substantial up-regulation in redox-related genes and B-ZIP transcripts. The report highlights the first use of bulked genotypes as replicated samples to compare the transcriptomes of obligate out-cross breeding populations in alfalfa. Three lines of Alfalfa (salt-tolerant CW064027, salt-tolerant Bridgeview, salt-sensitive Rangelander) were grown on 3 different concentrations of salt. For each cultivar-salt condition, 3 biological replicates were collected for a total of 27 samples.
2016-07-26 | E-GEOD-84825 | biostudies-arrayexpress
Project description:In this study, we aim to present a global view of transcriptome dynamics during various abiotic stresses in chickpea. We generated about 252 million high-quality reads from eight libraries (control, desiccation, salinity and cold stress samples for roots and shoots) using Illumina high-throughput sequencing GAII platform. We mapped the reads to the desi chickpea genome for estimation of their transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample. We collected different tissue samples (root and shoot tissues of 10-day-old seedlings subjected to control (kept in water), desiccation (transferred on folds of tissue paper), salinity (transferred to beaker containing 150 mM NaCl solution) and cold (kept in water at 4 M-BM-1 1M-BM-0C) stress for 5 h. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequenced data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to annotated chickpea genome using TopHat and fragments per exon kilobase per million (FPKM) was calculated using Cufflinks software for each gene in all the sample to measure their gene expression. Differential expression analysis was performed using Cuffdiff software. The differentially expressed genes during various abiotic stress conditions were identified.
2014-08-27 | E-GEOD-53711 | biostudies-arrayexpress
Project description:This project is aiming to examine the molecular response of the blue mussel (Mytilus edulis) to increased air temperatures and reduced salinity under laboratory conditions. There are 5 treatment groups (n=5), with group A representing the control (salinity 23percent salinity and temperature 5 degree celsius), group B ( 23percent salinity 30 degree celsius), group C (23percent salinity 33 degree celsius), group D (15percent salinity 5 degree celsius), group E (15percent salinity 30 degree celsius), group F (15percent salinity33 degree celsius), group G (5percent salinity 5 degree celsius).
2021-12-04 | E-MTAB-11178 | biostudies-arrayexpress