Surface of the tomatoes
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ABSTRACT:
PROVIDER: PRJNA506919 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Purpose: Circular RNAs (circRNAs) and microRNAs (miRNAs) play important roles in abiotic stress responses in plants. The aims of this study are to genome-widely identify the circRNAs, miRNAs and their targets in tomatoes at single heat, drought and their combination by high-throughput sequencing. Results: Following high-throughput sequencing, 765 miRNAs were identified in total with 335 conserved and 430 novel miRNAs in the 12 small-RNA libraries. Of these miRNAs, 32, 74 and 61 miRNAs were responsive to drought, heat and their combination, respectively. Following degradome sequencing, 50 sequences were identified as targets of 34 miRNAs in tomatoes at combined stress. Moreover, 467 circRNAs were identified in the 12 samples.
2020-02-20 | GSE121089 | GEO
Project description:Ripening is an important stage of fruit development to determine its quality as a diet. A tomato (Solanum lycopersicum) MADS-box transcription factor, RIPENING INHIBITOR (RIN), has been believed to serve as a regulator of ripening lying upstream of ethylene-dependent and ethylene-independent pathways. Here, we have conducted global gene expression analysis to comprehensively identify tomato genes whose expressions are affected by the rin mutation using microarray with RNA samples from the normal and rin mutant tomato fruits at the pre-ripening (mature green) and ripening (pink coloring) stages. By analysing this microarray data, we identified 342 of positively regulated and 473 negatively regulated genes by RIN, which showed >5 and <0.2 of the fold change ratio (FC) of normal fruits at the ripening stage relative to those at the pre-ripening stage, respectively, in a RIN-dependent manner. A chromatin immunoprecipitation (ChIP) analysis of the normal ripening tomatoes with the anti-RIN antibody revealed that the positively regulated gene set contained at least 13 direct RIN targets. We monitored global gene expression in normal (PK331 cultivar) and rin mutant (PK353 cultivar) tomatoes at the pre-ripening (mature green, G) and ripening (pink coloring, P) stages using microarray with three biological replicates for each sample.
2012-04-01 | E-GEOD-28564 | biostudies-arrayexpress
Project description:The Gut health in multiple joint osteoarthritis (MJOA) study leverages data from parallel community-based cohorts in humans and in pet dogs to elucidate the role of altered microbiota in MJOA. One hundred Johnston County Health Study human participants were 35 to 70 years of age at enrollment (2022-2023), self-identified as Hispanic, White, or Black, and lived in Johnston County, North Carolina. Demographic, clinical information, multiple joint radiographs, and stool samples for microbiome profiling by 16S rRNA gene sequencing were obtained from all participants. Similar data were collected from an independent group of pet dogs (N=115) from the local community, at the North Carolina State University (NCSU) College of Veterinary Medicine. The central hypothesis of the study is that intestinal permeability, with or without dysbiosis, is a major driver in the development and worsening of MJOA.
2025-04-01 | GSE293105 | GEO
Project description:3 fresh frozen Breast tumor from the University of North Carolina at Chapel Hill (UNC) were obtained from the UNC Tissue Procurement Facility under an IRB approved protocol. Each experimental sample was ssayed versus a common reference sample that was a modified version of the Stratagene Human Universal Reference (which was further augmented with a 1/10 amount of MCF7 mRNA and 1/10 amount of ME16C mRNA) Keywords = Agilent microarray Keywords = EGFR Keywords = keratin Keywords: parallel sample
2010-06-05 | E-GEOD-1319 | biostudies-arrayexpress
Project description:This was a controlled pilot study of 9 healthy adults admitted to the General Clinical Research Center at the University of North Carolina Hospital. After 3 days of clinical acclimatization, 6 subjects received a single 4g bolus dose or a placebo. Peripheral blood was collected on each day preceeding dosage, and then 6, 18, 24, 48, 72, and 96 hours post dosing. Total RNA was extracted and analyzed for differential gene expression on Agilent Human 1vA2 microarray chips.
2009-10-06 | GSE15158 | GEO
Project description:3 fresh frozen Breast tumor from the University of North Carolina at Chapel Hill (UNC) were obtained from the UNC Tissue Procurement Facility under an IRB approved protocol. Each experimental sample was ssayed versus a common reference sample that was a modified version of the Stratagene Human Universal Reference (which was further augmented with a 1/10 amount of MCF7 mRNA and 1/10 amount of ME16C mRNA) Keywords = Agilent microarray Keywords = EGFR Keywords = keratin Keywords: parallel sample
2004-10-15 | GSE1319 | GEO
Project description:Plasma was harvested from two cohorts of facility-matched germ free (GF) and specific-pathogen free (SPF) mice at the National Gnotobiotic Rodent Resource Center (NGRRC; North Carolina, USA). Plasma was then fractionated by size-exclusion chromatography using three tandem Superdex200 increase columns (Cytiva). Fractions corresponding with HDL were then pooled and concentrated prior to RNA isolation. Small RNA libraries were generated from total RNA using NextFlex V3 Small RNA Seq-kit (Perkin Elmer) according to manufacturer’s instructions. Equimolar amounts of each library were then pooled and sequenced on the NextSeq500 platform (Illumina). Individual libraries were then demultiplexed and analyzed with the TIGER analytical pipeline.
2022-06-29 | GSE206857 | GEO
Project description:Ripening is an important stage of fruit development to determine its quality as a diet. A tomato (Solanum lycopersicum) MADS-box transcription factor, RIPENING INHIBITOR (RIN), has been believed to serve as a regulator of ripening lying upstream of ethylene-dependent and ethylene-independent pathways. Here, we have conducted global gene expression analysis to comprehensively identify tomato genes whose expressions are affected by the rin mutation using microarray with RNA samples from the normal and rin mutant tomato fruits at the pre-ripening (mature green) and ripening (pink coloring) stages. By analysing this microarray data, we identified 342 of positively regulated and 473 negatively regulated genes by RIN, which showed >5 and <0.2 of the fold change ratio (FC) of normal fruits at the ripening stage relative to those at the pre-ripening stage, respectively, in a RIN-dependent manner. A chromatin immunoprecipitation (ChIP) analysis of the normal ripening tomatoes with the anti-RIN antibody revealed that the positively regulated gene set contained at least 13 direct RIN targets.
2012-04-02 | GSE28564 | GEO
Project description:As part of the West Virginia Chemical Spill research program, NTP evaluated three chemicals that were spilled into the Elk Rever in West Virginia for their ability to cause toxicity or biological changes in a short-term toxicogenomic study
2018-10-15 | GSE119833 | GEO
Project description:Regulatory divergence controlling wound-responsive gene expression in domesticated and wild tomatoes
| PRJNA361109 | ENA