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Predictive Models for Rice Quality Traits Using MATLAB
No full textThe purpose of this dataset is to provide predictive models for assessing rice quality traits (e.g., amylose content, viscosity profiles) and classifying rice types using Near-Infrared (NIR) spectroscopy. These models were developed in MATLAB (Matlab R2023a) using advanced methods, including Partial Least Squares (PLS), Partial Least Squares Discriminant Analysis (PLS-DA), Support Vector Machines (SVM), Machine Learning, and Artificial Neural Networks (ANN), applied to NIR spectra data. The PLS, iPLS, siPLS and mwPLS models were performed using MATLAB software and the iToolbox for MATLAB available from (http://www.models.life.ku.dk/itoolbox). The Classification toolbox (version 2.0), developed by Milano Chemometrics and QSAR Research Group (http//michem.disat.unimib.it/chm), was used for classification procedure.
This dataset includes the following components:
1. AMYLOSE_MODEL_FOOD_CHEMISTRY
A MATLAB-based predictive model for determining rice amylose content using NIR spectroscopy combined with PLS chemometric algorithms.
2. PLS-DA_SVM_MODELS
MATLAB-based predictive models for identifying different rice flour types using NIR spectroscopy with PLS-DA and SVM methods.
3. ANN_MODELS_ApSci
MATLAB-based predictive models for determining rice pasting parameters using NIR spectroscopy and Machine Learning tools.
4. ANN_MODELS_PASTING_FOODS
A MATLAB-based predictive model for evaluating rice quality based on grain physical parameters using Artificial Neural Network methods.
The .mat files are provided in a compressed .rar format and include the models with model performance metrics, ensuring reproducibility and facilitating model evaluation
Genes within eating quality and seed related QTLs with at least one HIGH impact SNP
No full textWhole-genome polymorphisms and phylogeny of rice varieties circulating in the European market
Online Resource 1 - Genes within eating quality and seed related QTLs with at least one HIGH impact SN
Glasshouse conditions monitoring for Vaccinium corymbosum exposed to soil microplastics
No full textThree-month monitoring of temperature and relative humidity in a glasshouse where Vaccinium corymbosum (cv. Ozarkblue) plants were exposed to soil polypropylene microplastic
GBA3 Sequence alignment data for Phylogenetic and CodeML analysis
No full text 1- Description of data files
Sequence alignment used for Phylogenetic and CodeML analysis described in https://doi.org/10.1038/s41598-020-68106-y.
Deposited files:
-Nucleotide sequence alignment_GBA3.fasta (fasta format);
-Nucleotide sequence alignment_GBA3.phy (phylip format input for PhyML3.0);
-nucleotide sequence alignment_GBA3_stats.txt (PhyML3.0 output with data and analysis description);
-nucleotide sequence alignment_GBA3_stout.txt (PhyML3.0 output describing smart model and phylogenetic analysis input parameters and calculation statistics);
-sms.csv (PhyML3.0 output smart model selection statistics);
-nucleotide_alignment_GBA3_tree.txt (Phylogenetic tree file in txt format)
2- Sequences
2.1 Sequence information
Nucleotide sequences obtained from NCBI nucleotide database or manually annotated using genomic information available in NCBI. All accession numbers of coding nucleotide sequences and genomic scaffolds used for manual gene annotation are available in supplementary table 5 of https://doi.org/10.1038/s41598-020-68106-y.
2.2 Naming rules
Each sequence presents a header with the following information for coding sequences
>3 letter code_ accession number or MA (manual annotation)
For pseudogenes
>3 letter code_PSEUDO
Correspondence between 3 letter code and species name can be found in supplementary table 5 of https://doi.org/10.1038/s41598-020-68106-y.
3-Sequence alignment and Phylogenetic analysis
All details are provided in the materials and methods of the publication. Coding nucleotide sequences were aligned in Geneious R7.1.9 using the translation align option (codon align) all remaning options were set to default. Poorly aligned codons were manually curated. Sequence alignment was inspected and columns contains 90% gaps were removed from the alignment. Premature stop codon in pseudogene and final stop codons were also removed. Final sequence alignment contained 97 sequences and a total of 1410 positions.
Phylogenetic analysis was calculated in PhyML 3.0 (http://www.atgc-montpellier.fr/phyml/) using smart model selection option and branch support was calculated using aBayes algorithm. Phylogenetic tree for selection was calculated using RAxML as described in https://doi.org/10.1038/s41598-020-68106-y
Sample and Procedure Metadata of Whole-Genome Sequencing of 20 Rice Varieties
No full textWithin the scope of the TRACE-RICE project, samples of 20 rice varieties were collected and ordered to sequence by Whole-genome sequencing.
This dataset contains metadata of the biological material used, the sequencing procedure and FastQC quality reports.
The raw 20 pairs of FASTQ files (40 in total), generated by paired-end high-throughoutput Illumina sequencing, are deposited and annotated in ENA under the PRJEB64146 project ID, with each pair corresponding to one rice variety (e.g., Albatros, Manobi, etc.)
Enzymatic characterization of soil extracts with five different mulch types in a Vaccinium virgatum plantation
No full textEvaluation of enzymatic properties soil extracts with five different mulch types where blueberry plants (Vaccinium virgatum cv. ‘Centra Blue’) have grown. Enzymatic measurements included (1) Dehydrogenase, an indicator of microbial activity; (2) Phosphatase, indicating phosphorus availability; (3) Glucosidase, a carbon cycle indicator; and (4) Arylsulfatase, a sulfur cycle indicato
Unveiling genetic REgulatory MOdules acting on the crosstalk between cork Development and EnvironmentaL factors
No full textCORK REMODEL emerges from the demonstrated engagement of its team to find novel solutions for fundamental research in cork oak genomics, focusing in cork development. We aim to apply state of the art data mining approaches to integrate available transcriptomic data, and predict pivotal gene regulatory modules and metabolic reactions acting during cork development and its crosstalk with environment (particularly drought
Replication Data for: Kinship Analysis and Pedigree Reconstruction of a Natural Regenerated Cork Oak (Quercus suber) Population
No full textThis dataset contains a set of SNPs identified in cork oak using the latest version of the Quercus suber L genome sequence which is not publicly available yet
Fatty acid profile of Hediste diversicolor subjected to different temperatures and salinities. Support dataset of the article https://doi.org/10.1016/j.aquaculture.2021.736871
No full textFatty acid profile (data presented as absolute abundances of fatty acids expressed as µg mg-1 of dry weight) of Hediste diversicolor (values of 7 replicates) subjected to different temperatures (24, 27 and 30 °C) and salinities (20 and 30) in a full factorial design (six experimental treatments: T24S20 – 24 °C salinity 20, T24S30 – 24 °C salinity 30, T27S20 – 27 °C salinity 20, T27S30 – 27 °C salinity 30, T30S20 – 30 °C salinity 20 and T30S30 – 30 °C salinity 30, sampled in two time points D14 – day 14 and D28 – day 28)
Morphological characterization of Vaccinium corymbosum exposed to soil microplastics under controlled conditions
No full textEvaluation of morphological response of Vaccinium corymbosum (cv. Ozarkblue) to two concentrations of polypropylene microplastics applied to the soil under controlled greenhouse conditions. Plant growth was monitored over two months through non-destructive measurements of cane number, height, width, and leaf number