RNA-Sequencing of PEG-stressed Sesame roots in drought sensitive and tolerant genotypes
Ontology highlight
ABSTRACT:
ORGANISM(S): Sesamum indicum
PROVIDER: GSE148340 | GEO | 2020/07/02
REPOSITORIES: GEO
Similar Datasets
Project description:RNA-Sequencing of PEG-stressed Sesame roots in drought sensitive and tolerant genotypes
| PRJNA623932 | ENA
Project description:Mature seeds of Arabidopsis thaliana are desiccation tolerant, but they lose DT while progressing to germination. Yet, there is a small developmental window during which DT can be rescued by treatment with polyethylene glycol (PEG). We used microarrays to identify relevant genes in the re-establishment of desiccation tolerance by PEG.
2015-08-25 | GSE64227 | GEO
Project description:The study was conducted to identify differentially expressed polyethylene glycol (PEG) induced water stress responsive genes in E. grandis. Forty day old rooted cutting of E. grandis was subjected to -0.225 MPa PEG treatment and total RNA was isolated from leaves of water treated control and PEG treated samples after three hours of treatment. The differential expression of water stress responsive genes was analyzed using microarray technique.
2016-01-01 | GSE73106 | GEO
Project description:The study was conducted to identify differentially expressed polyethylene glycol (PEG) induced water stress responsive genes in E. grandis. Forty day old rooted cutting of E. grandis was subjected to -0.225 MPa PEG treatment and total RNA was isolated from leaves of water treated control and PEG treated samples after three hours of treatment. The differential expression of water stress responsive genes was analyzed using microarray technique. Agilent two-color experiment, Organism: Eucalyptus,Custom Agilent Eucalyptus 8x60k Microarray Gene expression (AMADID: 59849 ) designed by Genotypic Technology Pvt.Ltd.
2016-07-03 | E-GEOD-73106 | biostudies-arrayexpress
Project description:We characterized the polyethylene glycol (PEG)-responding desiccome from the most geographically widespread Gram-positive nitrogen-fixing plant symbiont, i.e. Frankia alni, by next-generation proteomics.
2018-10-24 | PXD007226 | Pride
Project description:The integrative physiological and large-scale quantitative proteomic analysis of wheat chloroplast under salt and polyethylene glycol (PEG)-induced drought stresses by using label-free quantitative technique. We aim to reveal the underlying synergistic responsive mechanisms of wheat chloroplast proteome to salt and osmotic stresses, which could provide a more in-depth and comprehensive understanding on the roles of chloroplast proteome in abiotic stress response and defense.
2021-09-09 | PXD019453 | Pride
Project description:Polyethylene glycol (PEG) is one of the most common polymer contaminations in MS samples. At present, the detection of PEG and other polymers relies largely on manual inspection of raw data which is laborious and frequently difficult due to sample complexity and retention characteristics of polymer species in reversed phase chromatography. We developed a new strategy for the automated identification of PEG molecules from MSMS data using protein identification algorithms in combination with a database containing “PEG-proteins”. Through definition of variable modifications, we extend the approach for the identification of commonly used PEG-based detergents. We exemplify the identification of different types of polymers by static nanoESI-MSMS analysis of pure detergent solutions and data analysis using Mascot. Analysis of LC-MSMS runs of a PEG contaminated sample by Mascot identified 806 PEG-spectra originating from four PEG species using a defined set of modifications covering PEG and common PEG-based detergents. Further characterization of the sample for unidentified PEG species using error tolerant and mass tolerant searches resulted in identification of 3409 and 3187 PEG related MSMS spectra, respectively. We further demonstrate the applicability of the strategy for Protein Pilot and MaxQuant.
2018-05-28 | PXD009376 | Pride
Project description:Purpose: Current methods to repair ablation-type peripheral nerve injuries (PNIs) using peripheral nerve allografts (PNAs) often result in poor functional recovery due to immunological rejection as well as slow and inaccurate outgrowth of regenerating axon sprouts. In contrast, ablation-type PNIs repaired by PNAs using a multistep protocol, in which one step uses the membrane fusogen polyethylene glycol (PEG), permanently restore sciatic-mediated behaviors within weeks. Axons and cells within the PNA remain viable, even though outbred host and donor tissues are neither immunosuppressed nor tissue matched. PEG-fused PNAs exhibit significantly reduced T cell and macrophage infiltration, apoptosis, and expression of major histocompatibility complex I/II. In this study, we analyzed the coding transcriptome of PEG-fused PNAs to determine possible mechanisms underlying immunosuppression. Methods: Ablation-type sciatic PNIs in adult Sprague Dawley rats were repaired using PNAs and a PEG-fusion protocol combined with neurorrhaphy. Electrophysiological and behavioral recovery tests confirmed successful PEG-fusion of PNAs. RNA sequencing analyzed differential expression profiles of protein-coding genes between PEG-fused PNAs and NC PNAs (not treated with PEG) at 14d PO, along with Unoperated nerves. Sequencing results were validated by Quantitative Reverse Transcription PCR (RT-qPCR). Results: PEG-fused PNAs display significant downregulation of a great many gene transcripts associated with innate and adaptive allorejection responses. Many Schwann cell-associated transcripts are upregulated, and many cellular processes such as extracellular matrix remodeling, cell and tissue development are particularly enriched. Transcripts encoding several potentially immunosuppressive proteins (e.g. Thrombospondins 1 and 2) are upregulated in PEG-fused PNAs. Conclusions: This study is the first to characterize the coding transcriptome of PEG-fused PNAs, and identifies possible links between alterations of the extracellular matrix and suppression of the allorejection response. The results establish a molecular-basis to understand mechanisms underlying PEG-mediated immunosuppression.
2020-02-19 | GSE145504 | GEO
Project description:BackgroundSesame is an important oil crop due to its high oil, antioxidant, and protein content. Drought stress is a major abiotic stress that affects sesame production as well as the quality of sesame seed. To reveal the adaptive mechanism of sesame in response to water deficient conditions, transcriptomic and metabolomics were applied in drought-tolerant (DT) and drought-susceptible (DS) sesame genotypes.ResultsTranscriptomic analysis reveals a set of core drought-responsive genes (684 up-regulated and 1346 down-regulated) in sesame that was robustly differently expressed in both genotypes. Most enriched drought-responsive genes are mainly involved in protein processing in endoplasmic reticulum, plant hormone signal transduction photosynthesis, lipid metabolism, and amino acid metabolism. Drought-susceptible genotype was more disturbed by drought stress at both transcriptional and metabolic levels, since more drought-responsive genes/metabolites were identified in DS. Drought-responsive genes associated with stress response, amino acid metabolism, and reactive oxygen species scavenging were more enriched or activated in DT. According to the partial least-squares discriminate analysis, the most important metabolites which were accumulated under drought stress in both genotypes includes ABA, amino acids, and organic acids. Especially, higher levels of ABA, proline, arginine, lysine, aromatic and branched chain amino acids, GABA, saccharopine, 2-aminoadipate, and allantoin were found in DT under stress condition. Combination of transcriptomic and metabolomic analysis highlights the important role of amino acid metabolism (especially saccharopine pathway) and ABA metabolism and signaling pathway for drought tolerance in sesame.ConclusionThe results of the present study provide valuable information for better understanding the molecular mechanism underlying drought tolerance of sesame, and also provide useful clues for the genetic improvement of drought tolerance in sesame.
| S-EPMC6585049 | biostudies-literature
Project description:Naïve human embryonic stem cells (ESCs) are characterized by improved viability, proliferation, and differentiation capacity in comparison to traditionally derived primed human ESCs. However, currently used two-dimensional (2-D) cell culture techniques fail to mimic the three-dimensional (3-D) in vivo microenvironment, altering morphological and molecular characteristics of ESCs. Here, we describe the use of 3-D self-assembling scaffolds that support growth and maintenance of the naïve state characteristics of ESC line, Elf1. Scaffolds were formed via a Michael addition reaction upon combination of two 8-arm polyethylene glycol (PEG) polymers functionalized with thiol (PEG-8-SH) and acrylate (PEG-8-Acr) end groups. 3-D scaffold environment maintained the naïve state and supported long-term growth of ESCs. RNA-sequencing demonstrated significant changes in gene expression profiles between 2-D and 3-D grown cells. Gene Ontology analysis revealed upregulation of biological processes involved in the regulation of transcription and translation, extracellular matrix organization, and chromatin remodeling in 3-D grown cells. 3-D culture conditions also induced upregulation of genes associated with Wnt and focal adhesion signaling, while p53 signaling pathway associated genes were downregulated. Our findings for the first time provide insight into the possible mechanisms of self-renewal of naïve ESCs stimulated by the transduction of mechanical signals from the 3-D microenvironment.
2021-02-01 | GSE161306 | GEO