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2,785 results for “genotyping”
Pinna nobilis genotype table (Occitan coast)
<p>The fan mussel, <em>Pinna nobilis</em>, endemic to the Mediterranean Sea, is a critically endangered species facing mass mortality events in almost all of its populations, following the introduction of the parasite <em>Haplosporidium pinnae</em>. Such a unique pandemic in a marine organism, which spreads rapidly and with mortality rates reaching 100 %, could lead to the potential extinction of the species. Only few regions, involving lagoon habitats, remain healthy throughout entire Mediterranean Sea. This dataset was used to describes the genetic structure of <em>P. nobilis</em> across the Gulf of Lion, including confined locations such as lagoons and ports. This dataset contains the genotype, at 22 microsatellite loci, of total of 960 samples that were collected among 16 sites distributed at 8 localities.</p> <p>The results of the study are available in Peyran et al. (2021).</p> <p>Peyran, C., Boissin, E., Morage, T., Nebot-Colomer, E., Iwankow, G., & Planes, S. (2021). Genetic homogeneity of the critically endangered fan mussel, Pinna nobilis, throughout lagoons of the Gulf of Lion (North-Western Mediterranean Sea). <em>Scientific reports</em>, <em>11</em>(1), 1-12.</p> <p>Corresponding author: claire.peyran@gmail.com</p>
Dataset with SNP genotypes for local goat breeds of Mongolia (PLINK format)
<p>SNP genotyping was performed with Goat 50K BeadChip (Illumina Inc., USA) containing ~60 000 SNP. Quality control was performed by setting a cutoff of 0.5 for the GenCall and GenTrain scores. SNP dataset was filtered to remove poorly genotyped individuals, loci genotyped in <90% of individuals and rare alleles using PLINK 1.9 (Chang et al. 2015) with geno 0.1 --mind 0.1 --maf 0.05 plink parameters. To ensure that our analysis would not be affected by the presence of SNP in strong linkage disequilibrium we also filtered data with --indep-pairwaise 50 5 0.2 PLINK filter. </p>
dataset related to article "Italian cohort of Lafora disease: Clinical features, disease evolution, and genotype-phenotype correlations"
<p>dataset relateto to article at title</p>
Solanum section Lycopersicon (cultivated and wild tomato genotypes) trichome pictures
<p><strong>Stem trichome pictures of various genotypes from the <em>Solanum</em> section Lycopersicon:</strong></p> <pre><code class="language-markdown">| accession | species | accession nr | synonym | origin | |------------|--------------------------------|--------------|---------|-------------| | LA2172 | S. arcanum | TR0009 | - | Peru | | LA1401 | S. cheesmaniae f. minor | EA00652 | - | Ecuador | | LA1840 | S. chmielewskii | - | - | unknown | | LA2695 | S. chmielewskii | EA00759 | - | Peru | | LA0407 | S. habrochaites f. glabratum | EA00558 | - | Ecuador | | LA1777 | S. habrochaites f. hirsutum | EA00703 | - | Peru | | PI134418 | S. habrochaites f. glabratum | TR00015 | LYC38 | unknown | | LYC4 | S. habrochaites f. hirsutum | TR00017 | - | unknown | | LA1718 | S. habrochaites f. glabratum | EA00699 | LYC4934 | Peru | | PI127826 | S. habrochaites f. hirsutum | - | - | Peru | | LA1364 | S. huaylasense | TR00030 | - | Peru | | Moneymaker | S. lycopersicum | - | C32 | Netherlands | | LA4024 | S. lycopersicum | TA209 | - | unknown | | LA2133 | S. neorickii/L. parviflorum | EA00729 | - | Peru | | LA0735 | S. neorickii | TR00025 | LYC140 | unknown | | LA0716 | S. pennellii | EA00585 | - | Peru | | LA1278 | S. peruvianum/pimpinellifolium | TR00005 | - | unknown | | LA1954 | S. peruvianum | EA00713 | - | Peru | | LA1578 | S. pimpinellifolium | EA00674 | - | Peru |</code></pre> <p><strong>Pictures were taken in March 2018 following this two-step protocol:</strong></p> <pre><code class="language-markdown"># Making high-quality pictures of tomato trichomes This protocol is to take high-quality pictures of trichomes and stack them into one unique final picture. The stem from the 4th leaf from the top will be used to make a picture. This protocol is composed of two parts: - Firstly: take a series of pictures (15 to 30 pictures) using a stereomicroscope - Secondly: photo stacking using Photoshop # First part: taking pictures using the Leica MZFLII 1. Turn on the microscope zoom mechanism 2. Turn on the ebq 100 lamp and the Olympus Highlight 2000 lamp 3. Make sure no filter (e.g. dsRed) is applied 4. Open the Nikon NIS-Elements program. 5. Take a piece of stem and place it horizontally (---) under the microscope. . 6. Zoom out completely. 7. Zoom in at 10,000x on the side of the branch ("labeled 10.0 on the microscope). 8. Focus on a few trichomes. Get them as much as possible in focus. This is going to be your first picture (foreground). 9. Zoom in about a few trichome layers away. There should not be too much overlap between the different trichomes (otherwise they get merged together during the stacking phase). This will be your background. 10. Zoom out to go back to the foreground (= your first picture). 11. Depending on the number of trichomes in-between your foreground and background, you need to take a variable number of pictures. - If trichome density is high, then trichomes will overlap during the stacking meaning that you need to take more pictures (~30) and reduce the distance between your foreground and background. - If trichome density is low, then trichomes won't overlap and you need less pictures (~10) # Second part: alignment of pictures using Photoshop See the trichome layer photography protocol (PDF file)made by Maurice Heilijgers (August 2018).</code></pre> <p> </p>
Testing of resilient genotypes as rootstocks
<p>Previous TOMRES results highlighted resilient tomato genotypes under combined stress. This experiment aims to understand the impact of such genotypes when used as rootstocks on landrace and élite long shelf-life (LSL) accessions in the TOMRES Collection. The experiment was carried out under greenhouse conditions in spring 2018, at Agroilla facilities in Mallorca. Agronomic, fruit quality and plant physiology traits were measured in plants grown under control and combined stress (water+nutrient) treatments. Results denote the importance of some landrace genotypes used as rootstocks in increasing water-use efficiency and maintaining fruit traits in LSL landraces. Also, it is highlighted the different behaviour of landrace scions when grafted onto commercial and landrace rootstocks.</p>
Genome wide transcriptomic analysis of M82 genotype and one S. pennellii accession inoculated with the AM fungus Funneliformis mosseae under combined drought and low nutrient stress
<p>The aim of this experiment is to study transcriptome of tomato cv ‘M82’ and <em>S. pennellii </em>(LA5240) considering as factors combined nutrients and water stress, mycorrhization and the interaction between them. We grew plants under controlled conditions using <em>Funneliformis mosseae </em>as mycorrhizal fungus, a well-known symbiont for tomato. Combined water and nutrient stress was applied on 1 month old plants and maintained for 1 month, reducing up to 40% phosphorus, nitrogen and water provision. At the end of the experiment plant growth response was measured, AM colonization checked and RNA isolated from roots and sequenced. Data analysis is still in progress and only results produced until now are here provided (April-December 2018).</p>
Screening of the TOBC for genotypes with improved W/NUE under combined stress. MALLORCA EXPERIMENT.
<p>High-throughput tools were exploited to screen the TOBC (> 200 lines) for resilience to combined water and nutrient stress, to identify about 40 candidate accessions endowed with superior W/NUE constituting the TOMRES collection. The experiment was performed outdoors in summer 2017 at AGROILLA field. UIB screened TOBC under two treatments, one covering water (based on PET) and nutrient demands (well-watered, WW), and another reducing 50% water and 40% nutrient (N, P) as compared to WW (combined stress, CS). Tomato plants were visually and morphometrically measured (LMA, fruit weight and number); fruit quality, tolerance to pests and diseases, and W/NUE will be assessed, the former also with the use of δ13C. Results allowed the selection of ca. 40 lines and build the TOMRES collection.</p>
Comparative transcriptional profiling of two contrasting rice genotypes in response to rice stripe virus infection
GEO Series GSE11025. Oryza sativa. 12 samples. Type: Expression profiling by array.
RNA-Sequencing of PEG-stressed Sesame roots in drought sensitive and tolerant genotypes
GEO Series GSE148340. Sesamum indicum. 12 samples. Type: Expression profiling by high throughput sequencing.
Transcription profiling of wheat interacting with incompatible and compatible yellow rust in a Yr1-containing genotype
GEO Series GSE31761. Triticum aestivum. 9 samples. Type: Expression profiling by array.
Expression data from CD19-positive B-cells isolated from splenocytes from 8 week-old ingeneered mice from the indicated genotypes
GEO Series GSE69367. Mus musculus. 8 samples. Type: Expression profiling by array.
Genotype-dependent gene expression in barley
GEO Series GSE33393. Hordeum vulgare. 24 samples. Type: Expression profiling by array.
Transcriptomic analysis of maize developing earshoot from tropical maize hybrid genotypes native to Nigeria
GEO Series GSE18008. Zea mays. 24 samples. Type: Expression profiling by array.
Genotypic differences in water soluble carbohydrate metabolism in Triticum aestivum leaves
GEO Series GSE37675. Triticum aestivum. 16 samples. Type: Expression profiling by array.
Genotyping Porcine circovirus 3 (PCV-3) nowadays: does it make sense?
<p>Supplementary data 1. List of the accession numbers of the sequences used in the present study. Relevant metadata are also reported.<br> Supplementary figure 1. Maximum likelihood phylogenetic tree based on the ORF2 sequences. The tree nodes have been colour coded based on the respective bootstrap support.</p>
Genotypes original images HR
<p>Original images of six ornamental sunflower genotypes that were used in the ongoing research aimed at creating new ornamental varieties in Serbia, (45.26°N, 19.83°E). Varieties : ‘Neoplanta’, ‘Heliopa’, ‘CMS1 30’, 'Ring of Fire', ‘Pacino Gold’ and ‘Dwarf’ were used for ray floret color evaluation.</p>
Genotypes segmented images
<p>Segmented images of six ornamental sunflower genotypes that were used in the ongoing research aimed at creating new ornamental varieties in Serbia, (45.26°N, 19.83°E). Varieties : ‘Neoplanta’, ‘Heliopa’, ‘CMS1 30’, 'Ring of Fire', ‘Pacino Gold’ and ‘Dwarf’ were used for ray floret color evaluation.</p>
Genotypes original images LR
<p>Original images of six ornamental sunflower genotypes that were used in the ongoing research aimed at creating new ornamental varieties in Serbia, (45.26°N, 19.83°E). Varieties : ‘Neoplanta’, ‘Heliopa’, ‘CMS1 30’, 'Ring of Fire', ‘Pacino Gold’ and ‘Dwarf’ were used for ray floret color evaluation.</p>
Genotypes original images
<p>When using with the FloCIA software, these images should be in the folder: C:\FloCIA\Sunflowers\Genotypes original images.</p> <p> </p> <p> </p>
Task 4.1 Table 4.1.1_Seed index of soybean genotypes at NARDI in 2019
<p>At NARDI more than 100 genotypes from two core collections (Fundulea and Turda) were analysed for germination parameters.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.