DMPortal (BioData.pt)
Not a member yet
40 research outputs found
Sort by
Soil nematodes quantification and classification under long-term HDPE mulch application in a Vaccinium virgatum plantation
No full textQuantification and classification of soil nematodes by trophic group in a long-term field experiment assessing the effects of HDPE mulch application in a Vaccinium virgatum (‘Centra Blue’) plantation in southern Portugal. Nematodes were extracted from fresh soil samples and classified as Aphelenchus sp. (fungivores), Dorylaimida (omnivores), and Rhabditida (bacterivores
Characterization of polypropylene microplastics from agricultural mulch film
No full textMicroplastic particles (<5 mm) were generated from aged agricultural plastic film and used as soil contaminants in a controlled pot experiment with Vaccinium corymbosum (cv. Ozarkblue). The particles were produced through cryogenic grinding and sieving, and their size distribution was analyzed
recolha de material BS
No full textIdentificação das amostras recolhidas em Barradas da Serra de felogenio e folha
Replication Data for: New insights into adaptation and population structure of cork oak using genotyping by sequencing (Demultiplexed reads)
No full textDemultiplexed reads in fastq format for the linked paper
High impact genetic variants within 22 rice varieties
No full textA high quality polymorphisms dataset of genes and associated variants identified from germline variation calling workflow on the 22 rice varieties targeted in the TRACE-RICE project.
Raw sequencing data stored in ENA (PRJEB64146): https://www.ebi.ac.uk/ena/browser/view/PRJEB64146
Raw variant calling file data stored in EVA (PRJEB83571): https://www.ebi.ac.uk/eva/?eva-study=PRJEB83571
Online Resource 1 - Genes within eating quality and seed related QTLs with at least one HIGH impact SNP
Whole-genome polymorphisms and phylogeny of rice varieties circulating in the European market (under revision
Soil physicochemical properties evaluation under long-term HDPE mulch application in a Vaccinium virgatum plantation
No full textQuantification of soil physicochemical properties in a long-term field experiment assessing the effects of HDPE mulch application in a Vaccinium virgatum (‘Centra Blue’) plantation in southern Portugal. Soil samples were collected at 0-20 cm depth and analyzed for texture, pH, electrical conductivity, organic matter, organic carbon, macronutrients (P₂O₅, K₂O, Mg), exchangeable cations (Ca²⁺, Mg²⁺, K⁺, Na⁺), and micronutrients (Fe, Mn, Zn, Cu, B
Replication Data for: New insights into adaptation and population structure of cork oak using genotyping by sequencing (docker image)
No full textThis dataset contains the docker image containing the anlyses environment (and software) used in the title study.
Load it with the command:
docker load --input q.suber_gbs_data_analyses.tar
The container can then be started. In order to be able to access the results from your hosts system, the output directory should be mounted from the hosts system in the container with the following command:
docker run -v /full/path/to/output/dir:/home/qsuber/Qsuber_data_analysis/Analyses -i -t stunts/q.suber_gbs_data_analyses:latest (or another tag of your choice)
Make sure the Analyses directory is writable by the docker daemon (you will usually want to chmod 777 that directory).
If you wish to use different input files (.vcf and .loci files) you may add another mount parameter afer the first: -v /full/path/to/input/dir:/home/qsuber/Qsuber_data_analysis/ipyrad_outfiles
The input directory should contain the files: qsuber_clust95_lq3.loci and qsuber_clust95_lq3.vcf. If you want to user different filenames, you may do so, but don't forget to change them in the Makefile too.
Also note that the Makefile is configured to use 4 threads by default. You may want to change that parameter depending on your case. You can then start the analysis by running:
su qsuber
cd ~/Qsuber_data_analysis
make all
Wait a few days (depending on your system, of course), and the data analysis should be ready. Once this step is finished, run:
make blast
to perform BLAST searches of "non-neutral" markers against the Q. lobata genome
A Transcriptomic Approach to Understanding the Combined Impacts of Supra-Optimal Temperatures and CO2 Revealed Different Responses in the Polyploid Coffea arabica and Its Diploid Progenitor C. canephora
No full textUnderstanding the effect of extreme temperatures and elevated air (CO2) is crucial for mitigating the impacts of the coffee industry. In this work, leaf transcriptomic changes were evaluated in the diploid C. canephora and its polyploid C. arabica, grown at 25 °C and at two supra-optimal temperatures (37 °C, 42 °C), under ambient (aCO2) or elevated air CO2 (eCO2). Both species expressed fewer genes as temperature rose, although a high number of differentially expressed genes (DEGs) were observed, especially at 42 °C. An enrichment analysis revealed that the two species reacted differently to the high temperatures but with an overall up-regulation of the photosynthetic machinery until 37 °C. Although eCO2 helped to release stress, 42 °C had a severe impact on both species. A total of 667 photosynthetic and biochemical related-DEGs were altered with high temperatures and eCO2, which may be used as key probe genes in future studies. This was mostly felt in C. arabica, where genes related to ribulose-bisphosphate carboxylase (RuBisCO) activity, chlorophyll a-b binding, and the reaction centres of photosystems I and II were down-regulated, especially under 42°C, regardless of CO2. Transcriptomic changes showed that both species were strongly affected by the highest temperature, although they can endure higher temperatures (37 °C) than previously assumed
Physicochemical properties evaluation on soil extracts with five different mulch types in a Vaccinium virgatum plantation
No full textEvaluation of physicochemical properties on soil extracts with five different mulch types where blueberry plants (Vaccinium virgatum cv. ‘Centra Blue’) have grown. Properties such as particle size distribution (sand, silt, and clay), pH (H₂O), organic matter content, extractable nutrients (P, K, Mg, Fe, Mn, Zn, Cu, and B), exchangeable cations (Ca²⁺, Mg²⁺, K⁺, Na⁺), cation exchange capacity (SCT, CTCp(7.0), AP(7.0)), base saturation indices (GS, GSCa, GSMg, GSK), electrical conductivity (E.C.), and phthalate concentration were assesse
Drought impact on phellem development: identification of novel gene regulators and evidence of photosynthetic activity
No full textThis dataset contains the supplementary data (Figures and Tables) included in the manuscript "Drought impact on phellem development: identification of novel gene regulators and evidence of photosynthetic activity". Supplementary Figures includes additional data to support the manuscript, including plant growth and physiology measurements, histochemical analysis and accessory data from differential expression analysis. Supplementary Tables include primer sequences, lists of differentially expressed genes obtained using DESeq2 and Gene Ontology enrichment analysis obtained using GlueGO
Raw transcriptomic and phenotypic data is available in the following sources:
Raw reads: https://www.ebi.ac.uk/ena/browser/view/PRJEB66289
RNA-seq: https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-13376
Morphophysiological and chlorophyl fluorescence data: https://doi.org/10.34636/DMPortal/D8LBXX
Code/Software:
The R script used for differential gene expression analysis is available on GitHub: https://github.com/pedro-mb/CorkOakRNAseq
Additional data is available from the corresponding author, Pedro M. Barros, upon reques