Ontology highlight
ABSTRACT:
PROVIDER: PRJNA439242 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Manufacturing adulteration is the major cause of discrepancies between the declared and actual composition of food products. The use of high-throughput sequencing of DNA barcodes is a promising method to identify adulterants, but is not yet widely used in practice. Food pre-processing and differences in GC composition can lead to unequal amplification or complete loss of DNA barcode components, so the results of genomic analysis require an independent confirmation method. Perhaps the most promising way to increase the accuracy of food ingredient identification is to use an orthogonal method based on very different physical principles than DNA sequencing, which involves the analysis of other plant cell components, to verify the results of HTS analysis. In this work, we decided to evaluate the suitability of a multi-omic approach, including coupled DNA barcode HTS analysis and proteomic analysis, to estimate food fraud in herbal beverages. To resolve disputed discordant results obtained during genomic and proteomic investigation of samples, we used traditional botanical morphology method. Among the samples studied, the combined approach revealed two adulterations of Epilobium with Lythrum, which could be dangerous for the unsuspecting consumer.
2026-03-30 | PXD065433 | Pride
Project description:In plants, an increase in resource allocation to growth (primary metabolism) associated with the presence of neighbors is likely to reduce defense-related production (secondary metabolism), making plants more vulnerable to herbivory. Even though there is increasing evidence supporting this “trade-off hypothesis”, the underlying mechanisms are still unclear. Far red (FR) radiation reflected from plant tissues serves as an early warning signal of future competition, triggering a suite of plastic morphological adjustments that improve plant’s ability to compete for light in crowded populations. Recent evidence from our lab showed that, when competition signals are present, plant defenses are severely reduced. Besides direct effects of herbivory and competition signals on target plants, second order effects occurs on neighboring plants through plant volatiles (PVs) communication. PVs play a key role in plant-plant and plant-insect interactions, changing its content and composition in response to environmental conditions. To increase our understanding of the molecular mechanisms underlying those interacting signaling webs, we performed a field study with tomato plants (cv Moneymaker), in which plants of EMITTER plots (six plants plot-1) were subjected to herbivory (nine larvae of Spodoptera eridania plant-1) and competition signals (increased FR radiation) in a factorial design. Light treatment started 28 days after sowing (DAS), and herbivory treatment and volatiles conduction started 34 DAS. Volatiles were conducted from EMITTER to RECEIVER plots (five plants plot-1) using a 5 inch, 1.4 m long tube fitted with a computer-type fan. 40 and 45 DAS, larval performance was measured on EMITTER plots as well as naturally-occurring insect colonization on RECEIVER plots. Finally (46 DAS), samples for bulk phenolic content were taken on every plot, and plant material from 4th and 5th leaves was collected for microarray analysis. There were three real biological replicates. Keywords: Reference design
2008-02-13 | GSE10486 | GEO
Project description:This study was designed to construct and quantitatively characterize a synthetic promoter library in Escherichia coli. Promoter variants were assembled into the low-to-medium copy plasmid pSEVA221 to generate the p221-Plib library, in which each promoter was associated with a barcode sequence. The library was introduced into E. coli DH5α, and pooled transformants were cultured under selective conditions. Promoter activities were determined by sequencing barcode abundances from both RNA-derived cDNA and plasmid DNA libraries. The normalized RNA/DNA ratio was used as a quantitative measure of promoter activity, correcting for differences in sequencing depth, plasmid abundance, and clone representation. This dataset provides promoter activity profiles that can facilitate promoter selection and optimization for synthetic biology and metabolic engineering applications.
2026-02-16 | GSE318900 | GEO
Project description:HCC827 cells were barcoded using the ClonTracer lentiviral barcode library such that the majority of cells were infected with a single barcode. One million cells were expanded to ~120 million cells and split into 8 HYPERfasks. Two HYPERfasks were grown under DMSO and grown until confluence. In six HYPERfasks cells were grown under a GI90 concentration of one of two different inhibitors, gefitinib and trametinib (3 HYPERfasks each). Cells achieved confluence at 4 and 9 weeks for gefitinib and trametinib respectively. During this time, the medium and inhibitor were replenished weekly and DNA was extracted from the medium to track barcode content from dying cells.
2020-08-18 | E-MTAB-8841 | biostudies-arrayexpress
Project description:affy_tour_2010_21 - affy_tour_2010_21 - The aim of this project is to assess the possibility of implementing transcriptomic studies on sunflower plants grown in field assays. Data obtained from plants under drought in the glasshouse have already obtained. We intend to use these results as a template and see if the field offers the possibility of carrying these studies. In order to do so, treatment-effect as well as intra and inter-plot variability will be assessed.-Plants were grown in the field. The assay was arranged in plots with one genotype per plot. The assay was divided in two identically seized parts, containing the same number of plots. Starting from the capitule, flower # -3 was harvested in every plant. In some cases, several plants from the same plot were harvested. In other, plants from different plots were harvested. We expect that this sampling will allow us to assess intra- as well as inter-plot variability in the analysis of drought-driven gene expression modulation.
2012-09-01 | GSE36304 | GEO
Project description:Random DNA barcode could identified the functional atributes in immunophenotypic HSC fraction. Combined scRNA-seq with tracing random DNA-barcode could identifed specific molecular signature of the theses functional atributes.
2025-12-31 | GSE255989 | GEO
Project description:Seedbank study targeting plant barcode from soil samples
| PRJNA1123704 | ENA
Project description:Homo sapiens and Macaca fascicularis neural progenitor cell lines were transduced with a lentiviral MPRA (Massively Parallel Reporter Assay) library. MPRA barcode sequencing and RNA-seq was performed on the extracted RNA. MPRA data was used to compare activity of regulatory sequences across 75 mammalian species with a focus on primates and correlate these activities with the Phenotype of gyrencephaly.
2021-05-12 | E-MTAB-9952 | biostudies-arrayexpress