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Apr 19, 2018
Laloe, Denis, 2018, "Data associated to the paper "Genetic diversity and relationships among six local cattle populations in semi-arid areas assessed by a bovine medium-density data" (Boushaba et al, 2018)", https://doi.org/10.15454/HCFRWQ, Portail Data INRAE, V1
This data file consists of genotypes of 732 animals for 41183 markers. The animals belong to 23 populations. The file is a "csv" file where the field separator is ";". First line is a header. First column is the population identification the animal belongs to; following colums is...
Jun 25, 2018
Loudet, Olivier, 2018, "Raw phenotypic data obtained on the Arabidopsis RILs with the Phenoscope robots (Marchadier, Hanemian, Tisné et al., 2019)", https://doi.org/10.15454/OCOP9B, Portail Data INRAE, V1
This dataset gathers the main raw phenotypic data obtained and exploited in Marchadier, Hanemian, Tisné et al. (2019). It contains data from 4 RIL sets across 9 Phenoscope experiments. For each Phenoscope experiment, Recombinant Inbred Line (RIL) and Condition ('WW' = Well Watere...
Jun 25, 2018
Loudet, Olivier, 2018, "Genotypic description of the near isogenic lines (HIFs) used for QTL validation and significance of the observed segregating phenotypes (Marchadier, Hanemian, Tisné et al., 2019)", https://doi.org/10.15454/EORHL8, Portail Data INRAE, V1
Each row represents a single HIF and the genotype of the F7 RIL it originates from is indicated along the chromosomes with RIL ID, markers and genotypic conventions from Publiclines http://publiclines.versailles.inra.fr/rils/index (i.e. 'A' = Col allele; 'B' = alternate parental...
Jul 19, 2018
Chaumeil, Philippe; Fischer-Le Saux, Marion; Frigerio, Jean-Marc; Grenier, Eric; Rimet, Frédéric; Streito, Jean-Claude; Laval, Valérie; Franc, Alain, 2018, "R-Syst: a network providing curated molecular databases and data analysis tools for taxonomy and systematics (Prokaryotes and Eucaryotes)", https://doi.org/10.15454/OEDAUS, Portail Data INRAE, V1
R-Syst network deals about systematic and (meta) barcoding and provide curated molecular databases for species identification and provide tools for diagnosis and inventories. The stakes are at the same time a precise diagnosis of organisms of interest (for example pathogens detec...
Aug 3, 2018 - Omics Dataverse
Pauvert, Charlie; Buée, Marc; Laval, Valérie; Edel-Hermann, Véronique; Fauchery, Laure; Gautier, Angélique; Lesur Kupin, Isabelle; Vallance, Jessica; Vacher, Corinne, 2018, "DNA metabarcoding of a mock community of 189 fungal strains associated to plants and soils.", https://doi.org/10.15454/8CVWRR, Portail Data INRAE, V1
This sequence dataset (FASTQ format) was obtained by metabarcoding an artificial (mock) fungal community. The ribosomal internal transcribed spacer region 1 (ITS1) was amplified with the ITS1F / ITS2 primer pair and sequenced on an Illumina MiSeq platform (v3 chemistry, 2x250 bp)...
Aug 10, 2018
Vasselon, Valentin; Rimet, Frederic; Bouchez, Agnès, 2018, "Rsyst::diatom_rbcl_align_312bp database: a database adapted to DNA metabarcoding (version v7: 23-02-2018)", https://doi.org/10.15454/HYRVUH, Portail Data INRAE, V1
Method followed to obtain the Rsyst::diatom_rbcl_align_312bp database: 1/ Extraction of the 312bp rbcL barcode from the full Rsyst::diatom database rbcL alignment (using Diat_rbcL_108F and R3 primers). 2/ Sequences with ambiguities (N), homopolymers > 8 and length < 312bp are rem...
Oct 3, 2018
Mondy, Samuel, 2018, "GenoSol platform : A Logistic and Technical Platform for Conserving and Exploring Soil Microbial Diversity.", https://doi.org/10.15454/L7QN45, Portail Data INRAE, V1
The platform "GenoSol" was created by the UMR1347 AGROECOLOGIE at the INRA (French National Institute for Agronomic Research) of Dijon. This platform aimed to provide a logistics and technical structure dedicated to the acquisition, conservation, characterization and supply of ge...
Feb 7, 2019
Flori, Laurence, 2019, "Data associated to the paper "A genomic map of climate adaptation in Mediterranean cattle breeds" (Flori et al., Molecular Ecology, Epub 2018 Dec 29. doi: 10.1111/mec.15004)", https://doi.org/10.15454/PWKBFB, Portail Data INRAE, V1
This dataset consists of genotypes of 640 animals for 39921 variants (SNPs). Animals belong to 21 Mediterranean cattle populations. The compressed archive contains two files (in plink format): i) a genotyping data file named "MED_set.ped" (640 rows, 79848 columns) that contains,...
May 7, 2019 - Omics Dataverse
Pauvert, Charlie; Vallance, Jessica; Delière, Laurent; Buée, Marc; Vacher, Corinne, 2019, "DNA metabarcoding of foliar fungal communities in conventional and organic vineyards", https://doi.org/10.15454/3DPFNJ, Portail Data INRAE, V1
This sequence dataset (FASTQ format) was obtained by metabarcoding foliar fungal communities in conventional and organic vineyards. The ribosomal internal transcribed spacer region 1 (ITS1) was amplified with the ITS1F / ITS2 primer pair and sequenced on an Illumina MiSeq platfor...
May 9, 2019 - Omics Dataverse
Pauvert, Charlie; Vallance, Jessica; Delière, Laurent; Buée, Marc; Vacher, Corinne, 2019, "Bioinformatic scripts to assess the effect of the cropping system on both community and network α- and β-properties of fungal microbiota", https://doi.org/10.15454/NSHUAQ, Portail Data INRAE, V1
These bioinformatics scripts were applied to the sequences available at https://doi.org/10.15454/3DPFNJ. They are based on several softwares, including SparCC (Friedman and Alm 2012) and DADA2 (Callahan et al. 2016). The code corresponds to R and R markdown files. These scripts w...
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