AndreaBozzo/ceres-open-data-index huggingface dataset:
Frimouss project

[Lien vers la fiche source] Fruit features : Fruit growth has been measured from anthesis to harvest on plants with regular crop load. The anthesis date have been observed in order to describe the data collected according to days and degree-days from anthesis. Fruit growth has been monitored using non-destructive measurements that measure fruit dimensions (diameters, length) and using destructive sampling to estimate the fruit fresh and dry mass accumulation. Metabolites : Biomass compounds and accumulated metabolites that constitute the major carbon sinks have been quantified and their contents expressed on fresh- and dry weight bases. Total proteins, nucleic acids and starch have been quantified via spectrophotometric or fluorimetric measurements after specific extraction, preparation and calibration. Culture location : INRA UE0695 UERI (Unite Experimentale Recherches Intégrees - Gotheron)
Frimouss Kiwi

[Lien vers la fiche source] Fruit features : Fruit growth has been measured from anthesis to harvest on plants with regular crop load. The anthesis date have been observed in order to describe the data collected according to days and degree-days from anthesis. Fruit growth has been monitored using non-destructive measurements that measure fruit dimensions (diameters, length) and using destructive sampling to estimate the fruit fresh and dry mass accumulation. Metabolites : Biomass compounds and accumulated metabolites that constitute the major carbon sinks have been quantified and their contents expressed on fresh- and dry weight bases. Total proteins, nucleic acids and starch have been quantified via spectrophotometric or fluorimetric measurements after specific extraction, preparation and calibration. Culture location : INVENIO, Ste Livrade, France
Frimouss Grapevine

[Lien vers la fiche source] Fruit features : Fruit growth has been measured from anthesis to harvest on plants with regular crop load. The anthesis date have been observed in order to describe the data collected according to days and degree-days from anthesis. Fruit growth has been monitored using non-destructive measurements that measure fruit dimensions (diameters, length) and using destructive sampling to estimate the fruit fresh and dry mass accumulation. Metabolites : Biomass compounds and accumulated metabolites that constitute the major carbon sinks have been quantified and their contents expressed on fresh- and dry weight bases. Total proteins, nucleic acids and starch have been quantified via spectrophotometric or fluorimetric measurements after specific extraction, preparation and calibration. Culture location : INRA UMR EGFV (Ecophysiologie et Genomique Fonctionnelle de la Vigne, Bordeaux-Aquitaine)
Transposable Elements prediction and annotation in the C. elegans genome

[Lien vers la fiche source] This datasets contains all the essential files produced during the TE prediction, annotation, and post-processing in the C. elegans genome (e.g. TE consensus library, TE annotations, and associated statistics). Also contains the global workflow (used command lines), the REPET configuration files (with parameters) used for this analysis and the in-house python script used to identify canonical TE annotations using TE consensus library and draft TE annotation (REPET output). Download: In order to preserve the folder and file tree structure (easier to reproduce the analyses), select all the files and click on download (original format). The download of a .zip archive should start. Once downloaded, extract the contents of the archive.
Frimouss Apple

[Lien vers la fiche source] Fruit features : Fruit growth has been measured from anthesis to harvest on plants with regular crop load. The anthesis date have been observed in order to describe the data collected according to days and degree-days from anthesis. Fruit growth has been monitored using non-destructive measurements that measure fruit dimensions (diameters, length) and using destructive sampling to estimate the fruit fresh and dry mass accumulation. Metabolites : Biomass compounds and accumulated metabolites that constitute the major carbon sinks have been quantified and their contents expressed on fresh- and dry weight bases. Total proteins, nucleic acids and starch have been quantified via spectrophotometric or fluorimetric measurements after specific extraction, preparation and calibration. Culture location : INRA UE0695 UERI (Unite Experimentale Recherches Intégrees - Gotheron)
MERCI effector-enriched motifs in the 100 first amino acids of M. incognita proteins

[Lien vers la fiche source] MERCI effector-enriched motifs in the 100 first amino acids of M. incognita proteins M. incognita proteins with at least one of the 4 motifs identified as enriched in the known effector proteins as described in (Vens, Rosso, Danchin, Bioinformatics, 2011)
Negative set used to identify enriched motif in effectors regulatory regions

[Lien vers la fiche source] As negative set, we selected 167 M. incognita genes from an Orthofinder analysis (Emms & Kelly, 2019) previously performed on 64 genomes, including 62 nematodes and two outgroup tardigrade species (Grynberg et al., 2020). The selection criteria were as follows: (i) the vast majority (163 genes) came from orthogroups conserved in at least 80% of the species and 85% of the Tylenchida and did not form multigene families. Being widely conserved across nematodes, including in many non phytoparasitic species and not forming multigene families, these genes are more likely involved in core housekeeping functions than coding for effector proteins. (ii) four genes specific to root-knot nematodes but bearing no signal peptide for secretion, including one gene specific to M. incognita.
Frimouss Eggplant

[Lien vers la fiche source] Fruit features : Fruit growth has been measured from anthesis to harvest on plants with regular crop load. The anthesis date have been observed in order to describe the data collected according to days and degree-days from anthesis. Fruit growth has been monitored using non-destructive measurements that measure fruit dimensions (diameters, length) and using destructive sampling to estimate the fruit fresh and dry mass accumulation. Metabolites : Biomass compounds and accumulated metabolites that constitute the major carbon sinks have been quantified and their contents expressed on fresh- and dry weight bases. Total proteins, nucleic acids and starch have been quantified via spectrophotometric or fluorimetric measurements after specific extraction, preparation and calibration. Culture location : INVENIO, Ste Livrade, France
M. incognita predicted secreted proteins

[Lien vers la fiche source] To identify putative secreted proteins in the M. incognita protein set (Blanc-Mathieu et al. 2017), we searched for predicted signal peptides (SP) for secretion using SignalP v4 (Petersen, Brunak, von Heijne, & Nielsen, 2011). This program improves the differentiation between transmembrane regions present in the N-terminal part of a protein and the presence of a peptide signal. In order to further eliminate this potential problem, predicted signal peptides were cropped, with the remaining part of the proteins subjected to TMHMM (Krogh, Larsson, von Heijne, & Sonnhammer, 2001) for prediction of transmembrane regions. Proteins bearing a predicted SP and no transmembrane region were considered as putative secreted proteins. A separate list of predicted secreted proteins specific to plant-parasitic nematode species, according to orthofinder is also provided.
Frimouss Pepper

[Lien vers la fiche source] Fruit features : Fruit growth has been measured from anthesis to harvest on plants with regular crop load. The anthesis date have been observed in order to describe the data collected according to days and degree-days from anthesis. Fruit growth has been monitored using non-destructive measurements that measure fruit dimensions (diameters, length) and using destructive sampling to estimate the fruit fresh and dry mass accumulation. Metabolites : Biomass compounds and accumulated metabolites that constitute the major carbon sinks have been quantified and their contents expressed on fresh- and dry weight bases. Total proteins, nucleic acids and starch have been quantified via spectrophotometric or fluorimetric measurements after specific extraction, preparation and calibration. Culture location : INVENIO, Ste Livrade, France
Annotated list of species used in this study

[Lien vers la fiche source] Annotated list of the 63 species used in the Orthofinder comparative analysis of nematodes (61 species) and two tardigrade species as out-groups. Description: Lines 1-64, definition of columns - Abbrev Species: abbreviated species name. Species identifiers used in all the Orthofinder analysis. - Species: Latin species name. - BUSCO%: percentage of core eukaryotic proteins (odb9) found in full length by BUSCO V3 in the proteome. - Proteins: number of predicted proteins - Taxo: taxonomic group - Hclade: Helder Clade classification according to 'Van Megen et al. A phylogenetic tree of nematodes based on about 1200 full-length small subunit ribosomal DNA sequences. Nematology. 2009' - Bclade: Blaxter Clade classification according to '' - Lifestyle: feeding style of the species - Source: origin of the proteome file - Reference: bibliographic references associated to the species genome paper Lines 66-108: full bibliographic refernces with Authors, Title, Journal and Year
Frimouss Peach

[Lien vers la fiche source] Fruit features : Fruit growth has been measured from anthesis to harvest on plants with regular crop load. The anthesis date have been observed in order to describe the data collected according to days and degree-days from anthesis. Fruit growth has been monitored using non-destructive measurements that measure fruit dimensions (diameters, length) and using destructive sampling to estimate the fruit fresh and dry mass accumulation. Metabolites : Biomass compounds and accumulated metabolites that constitute the major carbon sinks have been quantified and their contents expressed on fresh- and dry weight bases. Total proteins, nucleic acids and starch have been quantified via spectrophotometric or fluorimetric measurements after specific extraction, preparation and calibration. Culture location : INRA UMR 1115 PSH (Plantes et Systemes de culture Horticoles, Avignon)
Taxonomic distribution of M. incognita Diamond hits against the NCBI's nr library

[Lien vers la fiche source] Taxonomic distribution of M. incognita Diamond hits against the NCBI's nr library. The taxonomy has been determined by Diamond LCA algorithm via outformat 102. Two reports are available: 1- all the M. incognita proteins as queries 2- PPN-specific M. incognita proteins as queries The first column represent the number of hist returning hits of the taxonomic entity under consideration. All the other columns represent the hierarchy of the taxonomic lineage. Krona graphs providing a visual and interactive taxonomic distribution of the Diamond hits are also available for each report. (all proteins and PPN-specific only).
TE-related genes: annotation, characterisation, and expression.

[Lien vers la fiche source] This dataset contains the gene analysis workflow used to evaluate the genes expression and to find the genes potentially involved in the TEs transposition machinery. Also, it contains the gene annotation file (bed format), the proteome stem from (https://doi.org/10.1371/journal.pgen.1006777), and several gene expression tables based on the previously mentioned study's transcriptome. Finally, it contains the scripts, output table and genes lists from the proteome analysis which aim was to identify genes potentially linked to the TE transposition machinery based on extensive HMM profile search (concatenation of pfam32 and GyDB2.0). Download: In order to preserve the folder and file tree structure (easier to reproduce the analyses), select all the files and click on download (original format). The download of a .zip archive should start. Once downloaded, extract the contents of the archive.
Transposable Elements prediction and annotation in the M. incognita genome

[Lien vers la fiche source] This datasets contains all the essential files produced during the TE prediction, annotation, and post-processing in the M. incognita genome (e.g. TE consensus library, TE annotations, and associated statistics). Also contains the global workflow (used command lines), the REPET configuration files (with parameters) used for this analysis and the in-house python script used to identify canonical TE annotations using TE consensus library and draft TE annotation (REPET output). Download: In order to preserve the folder and file tree structure (easier to reproduce the analyses), select all the files and click on download (original format). The download of a .zip archive should start. Once downloaded, extract the contents of the archive.
TE polymorphisms detection and analysis

[Lien vers la fiche source] This dataset contains i) output files from "Kozlowski D. 2020a. Transposable Elements prediction and annotation in the M. incognita genome. Portail Data INRAE [Internet]. Available from: https://doi.org/10.15454/EPTDOS", "Kozlowski D. 2020b. Transposable Elements prediction and annotation in the C. elegans genome. Portail Data INRAE [Internet]. Available from: https://doi.org/10.15454/LQCIW0", and "These analyses are presented in detail in Kozlowski D, Da Rocha M, Danchin E. 2020. TE-related genes: annotation, characterisation, and expression. Portail Data INRAE [Internet]. Available from: https://doi.org/10.15454/DLDJVF" ; ii) popoolationTE2 workflow used to detect polymorphism across M. incognita's isolates and evaluate the tool error rate; iii) the global analysis workflow and associated results; and iv) the produced figures. Download: In order to preserve the folder and file tree structure (easier to reproduce the analyses), select all the files and click on download (original format). The download of a .zip archive should start. Once downloaded, extract the contents of the archive.
M. incognita candidate effector proteins

[Lien vers la fiche source] Accession numbers of M. incognita candidate effectors. These proteins are predicted to be secreted based on the presence of a signal peptide for secretion and absence of transmembrane domains. Furthermore at least one motif known to be enriched in effector proteins is present in the 100 first amino acids. A separate subset of those specific to plant-parasitic nematode species is also provided.
Meloidogyne incognita Interproscan annotation

[Lien vers la fiche source] Interproscan annotation on the 43,718 predicted proteins in the genome of the root-knot nematode Meloidogyne incognita (Blanc-Mathieu et al. 2017, PLoS Genetics). vesrion used: interproscan-5.29-68.0 options used: -dp Disables use of the precalculated match lookup service = all match calculations are run locally. -iprlookup lookup of corresponding InterPro annotation -goterms lookup of corresponding Gene Ontology annotation -pa lookup of corresponding Pathway annotation -f TSV format the results in tab-separated values
SLA - Données essentielles de la commande publique - 2019

Liste des marchés publics conclus en 2019 par Saint-Louis Agglomération (objet du marché, montant, type de procédure, date de notification et de publication, durée, etc). Ce jeu de données respecte à plus de 90% le Socle Commun des Données Locales (SCDL) pour le format du contenu et à 100% pour la structure. Personnes référentes des données : Marion Perez - Service Open Data - 03.89.70.46.67 Catherine Wiss - Service Commande publique - 03.89.70.90.72
Enriched gene ontology terms in upregulated genes at the transition from adult females to eggs

[Lien vers la fiche source] Analysis of differentially represented (over and under) Gene Ontology (GO) terms in the genes showing significant up-regulation at the transition between the eggs and the pre-parasitic J2 stage. GO over and under representation of terms are according to the hypergeometric test as implemented in the GofuncR Bioconductor package (https://www.bioconductor.org/packages/release/bioc/html/GOfuncR.html). Results are separated by: - Molecular Function - Biological Process - Cellular Component And, in each ontology, under, over and all differentially expressed GO terms are given. All the files are in table separated values format, with the last common providing the accession numbers of proteins annotated with the GO term under consideration.
Enriched gene ontology terms in upregulated genes at the transition from J3-J4 larvae to adult females

[Lien vers la fiche source] Analysis of differentially represented (over and under) Gene Ontology (GO) terms in the genes showing significant up-regulation at the transition between the J3-J4 mixed stages and the adult female stage. GO over and under representation of terms are according to the hypergeometric test as implemented in the GofuncR Bioconductor package (https://www.bioconductor.org/packages/release/bioc/html/GOfuncR.html). Results are separated by: - Molecular Function - Biological Process - Cellular Component And, in each ontology, under, over and all differentially expressed GO terms are given. All the files are in table separated values format, with the last common providing the accession numbers of proteins annotated with the GO term under consideration.
Expression clusters of differentially-expressed M. incognita genes

[Lien vers la fiche source] Distribution of the 12,461 differentially expressed M. incognita genes on 8 expression clusters (named A to H). Files named ClusterA-H.txt list the genes present in each expression clusters. The file named Clusters.xlsx summarizes the distribution of all these genes across the 8 clusters as well as gene models corresponding to known DG and SvG effectors. Gene expression clusters have been obtained by divisive hierarchical clustering.
Centros asistenciales

This dataset is linked to the following visualization: [Visualization - Centros asistenciales] Este dataset hace referencia a centros relacionados con residencias de ancianos, centros de asistencia social, albergues y otros tipos de centros de distinta titularidad que se pueden ver en la información. El dataset se ordena numéricamente por su valor ascendente. Los datos se han obtenido de la Encuesta de Infraestructura y Equipamientos Locales, en su fase de 2021.
Extracellular vesicles produced by human and animal Staphylococcus aureus strains share a highly conserved core proteome

[Lien vers la fiche source] The Extracellular Vesicle (EV) proteomes of five Staphylococcus aureus (S. aureus) strains originating from human, bovine, and ovine hosts were characterised thanks to proteomics. EVs were purified from supernatants of early stationary S. aureus cultures by a sucrose density gradient. Protein trypsin digestion were performed in solution. The data set contains 15 files of NanoLC-MS/MS analysis, acquired on a Qexactive mass spectrometer. Design: 5 classes (S.aureus human strain: "MW2", S. aureus bovine strains: "NB305" and "RF122", S.aureus ovine strains: "O11" and "O46"). 3 biological replicates.
Vitis Organ ontology

[Lien vers la fiche source] The file lists the terms that are recommended to be used to describe the different parts of a grapevine plant. It also contains cross references with other plant ontology databases. This thesaurus was established in the framework of the European COST 858 "Integrape" action. The main objective was to establish a common vocabulary to make the data obtained in the experiences on grapevines FAIR (findable, accessible, interoperable and reusable). Other ontologies used: : http://browser.planteome.org/ , https://www.ebi.ac.uk/ols/ontologies/po, https://www.ebi.ac.uk/ols/ontologies/bto
Dataset on model cheeses composition, rheological and sensory properties, from six different projects exported from BaGaTel database.

[Lien vers la fiche source] This dataset corresponds to the raw data which will be used for a datapaper (in preparation for Data in Brief) and a publication (in preparation for International Dairy Journal). This dataset consists in a Microsoft excel Worksheet containing 4 sheets: 1) information on variables, 2) whole dataset, 3) missing data estimation, 4) dataset+estimated-data, 5) dataset_PCA-68samples, 6) correlation-matrices-68samples, 7) dataset_chewing-activity, 8) correlation-matrices_Chewing, 9) dataset_22samples-fatty, 10) correlation-matrix_22samples.
Mataderos

This dataset is linked to the following visualization: [Visualization - Mataderos] Listado de mataderos que abastecen carne exclusivamente a la población de sus términos municipales, con indicación de la titularidad, gestión de las instalaciones, ámbito territorial y tipo de ganado de sacrificio. El dataset se ordena numéricamente por su valor ascendente. Los datos se han obtenido de la Encuesta de Infraestructura y Equipamientos Locales, en su fase de 2021.
Parques y jardines

This dataset is linked to the following visualization: [Visualization - Parques y jardines] Zonas públicas como parques y jardines que puedan ser usados por el conjunto de los vecinos para su recreo y esparcimiento. El dataset se ordena numéricamente por su valor ascendente. Los datos se han obtenido de la Encuesta de Infraestructura y Equipamientos Locales, en su fase de 2021.
Edificios públicos sin uso

This dataset is linked to the following visualization: [Visualization - Edificios públicos sin uso] Edificios de propiedad pública, hoy sin uso, y que puedan ser recuperados para la colectividad. En el caso de edificios parcialmente sin uso, se detallará solamente la parte que no está usada. No figuran los solares o edificios en ruinas que no pueden ser rehabilitados. Para visualizar su ubicación es necesario ampliar el visor del mapa hasta localizar una superficie de color marrón que nos indica la situación del edificio. El dataset se ordena numéricamente por su valor ascendente. Los datos se han obtenido de la Encuesta de Infraestructura y Equipamientos Locales, en su fase de 2021.