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1,155 results for “loci”
Fig. 2 in The Dynamics Of Genetic Structure Of Round G O B Y N E O G O B I U S M E L A N O S T O M U S (Pa L L A S) Groupings In The Odessa Bay Of The Black Sea Utilizing Biochemical Marker Loci
Fig. 2. Frequencies of S-alleles by polymorphic locus of myogene 3 in round goby groupings from different parts of the Odessa Bay * – significant deviation of allele frequencies in round goby groupings from the south and the north part of the Odessa Bay in 2013 and 2014 (Р = 0,05); # – significant deviation of allele frequencies in round goby groupings from the south part of the Odessa Bay in 2013-2014 in comparison to 2015 (Р = 0,05).
FIGURE 1 in Development of microsatellite loci and population genetics in the bumblebee catfish species Pseudopimelodus atricaudus and Pseudopimelodus magnus (Siluriformes: Pseudopimelodidae)
FIGURE 1 | Sampling sites of Pseudopimelodus magnus and P. atricaudus in the middle and lower sectors of the Cauca River.
Fig. 2. Chromatograph comparing original and redesigned primers for Ccmic3 in Inheritance of fifeen microsatellite loci in Ceratitis capitata (Diptera: Tephritidae)
Fig. 2. Chromatograph comparing original and redesigned primers for Ccmic3 on sample A1-F1-07, Family A1. Both reactions were run simultaneously on the same fragment analysis plate using the same PCR conditions, DNA concentrations, and dilution factor. a) Chromatograph of progeny exhibiting an allele call of 74/74. Parents are 74/76 and 76/76. The observed 76 bp peak was considered to be weak. Cloning and sequencing confirmed the existence of this 76 bp fragment. b) Chromatograph of the same progeny as in Fig. 2a now exhibiting an allele call of 72/74 afer primer modification. Parents are now 72/74 and 74/74. The observed 74 bp peak is more pronounced compared to the previous 76 bp call. The intensity of the 74 bp peak also increased while the other 3 visible peaks decreased. This suggests an increase in adenylation has occurred.
Fig. 1 in Inheritance of fifeen microsatellite loci in Ceratitis capitata (Diptera: Tephritidae)
Fig. 1. Sequence alignment of Ccmic3 with original primer design. Top two sequences are genotypes of 74 bp allele and bottom two sequences are genotypes of the 76 bp allele. One extra thymine residue on the 5' end appeared in 8 of the 8 clones for this allele leading to difficulties in scoring this locus. Redesign of the forward primer by adding the extra guanines provided better resolution in scoring. Lower case sequence represents the Topo 2.1 vector just past the EcoRI in the multiple cloning site.
Fig. 3 in Inheritance of fifeen microsatellite loci in Ceratitis capitata (Diptera: Tephritidae)
Fig. 3. Comparing artifactual bands to actual bands to determine allele as observed at the Ccmic25 locus. a) Chromatograph of sample exhibiting an artifactual band can be observed at the 136 bp peak. The geometric shape and configuration is not consistent with those of microsatellites. b) This chromatograph shows the characteristic high peak followed by a low peak expected when making a call around the 137 bp peak. To the lef of both peaks are very low broad bands, commonly observed during analysis. In homozygote individuals, these peaks may extend higher and resemble an artifactual band similar to what was observed in Fig. 3a.
Fig 5 in Using mating-type loci to improve taxonomy of the Tuber indicum complex, and discovery of a new species, T. longispinosum
Fig 5. Phylogenetic relationships among Asian black truffles based on three combined datasets (ITS, β-tublin, and TEF1-α). The phylogram was obtained by maximum likelihood inference under the TN93+I model. SH-aLRT values and Bayesian posterior probabilities are shown as ML/BPP.
Fig. 2 in Testing microsatellite loci and preliminary genetic study for Eurasian otter in South Korea
Fig. 2. Locations of sampling for tissue (1. Hoengseong-gun, Gangwon-do, 2. Uljin-gun, Gyeongsangbuk-do, 3. Jeongeup-si, Jeollabukdo, 4. Muju-gun, Jeollabuk-do, 5. Hampyeong-gun, Jeollanam-do).
Microsat Data for 'Simulated Disperser Analysis: determining the number of loci required to genetically identify dispersers'
<p>Microsattelite data from 94 samples (<em>Stunus vulgaris</em>) from 3 populations and including 29 loci. Used in the paper 'Simulated Disperser Analysis: determining the number of loci required to genetically identify dispersers'. </p>
Genome-wide association meta-analysis of 30,000 samples identifies seven novel loci for quantitative ECG traits
<p><strong>Introduction</strong></p> <p>These are the <em>Summary Level-data</em> as presented in:</p> <p>"Genome-wide association meta-analysis of 30,000 samples identifies seven novel loci for quantitative ECG traits". Eur J Hum Genet. 2019 Jan 24. doi: 10.1038/s41431-018-0295-z.<em> [Epub ahead of print]</em></p> <p>If you use these data please cite the corresponding manuscript, which can be downloaded here: <a href="http://em.rdcu.be/wf/click?upn=lMZy1lernSJ7apc5DgYM8eFz0euOx0-2B13Abimi4Sb0A-3D_2NNavOiAD9A7CPFnsa04dGla3sU002fLfkDtL-2FhGlad0GuoM-2B3OlDb0C5GiEhwIvtH7ba4KKF45ipTOFodx6CqvVvoP2GQ992sPGoV9ZPWIe04tUd8-2BGWey0In0TXPII5zK-2Bfp8Wk9TpEqEcSd-2BEmywqZc8o5TW4xGPXZqmchfUH8chy3P4SEtpzHXMG1LwsIYrKfwegqTXG85RAJPr-2B21Tk9SobtpvFs0frMkJ4ekKsl33ryoZfFPk1byjQunJYn4-2BB0iqMgGs6cXv0AOgAxg-3D-3D">https://rdcu.be/bh8mu</a>. When you have any questions or comments regarding this study or these files, please contact me via:</p> <p>Jessica van Setten, PhD | <em>Department of Cardiology, University Medical Center Utrecht, Utrecht University</em> | j.vansetten [at] umcutrecht [dot] nl</p> <p> </p> <p><strong>Files and description</strong></p> <p>There are four files available:</p> <ol> <li>RR_summary_Sept2018.txt.gz - gzipped file containing all the (unfiltered) meta-analysis results for RR interval</li> <li>PR_summary_Sept2018.txt.gz - gzipped file containing all the (unfiltered) meta-analysis results for PR interval</li> <li>QT_summary_Sept2018.txt.gz - gzipped file containing all the (unfiltered) meta-analysis results for QT interval</li> <li>QRS_summary_Sept2018.txt.gz - gzipped file containing all the (unfiltered) meta-analysis results for QRS duration</li> </ol> <p>All these files have the same lay-out and are gzipped. The reference used for meta-analysis of GWAS was Genome of the Netherlands v4. </p> <ul> <li><em>SNP</em> - variantID (rsID), please note that few hundred variants do not have an rsID, but are NA instead. These can still be identified by chromosome and position.</li> <li><em>CHR</em> - chromosome numbers [1-22 and X].</li> <li><em>POS</em> - base pair position, hg19 / build37.</li> <li><em>CODED_ALLELE</em> - coded allele, <em>i.e.</em> the effect allele, as represented (and harmonized) across cohorts. Note that this is not necessarily the minor allele.</li> <li><em>NON_CODED_ALLELE</em> - the other allele, <em>i.e.</em> the non-effect allele.</li> <li><em>CODED_ALLELE_FREQ</em> - coded allele frequency, <em>i.e.</em> the effect allele frequency. Note that this is not necessarily the minor allele frequency.</li> <li><em>BETA</em> - beta from the fixed-effects model.</li> <li><em>SE </em>- standard error from the fixed-effects model.</li> <li><em>P </em>- P-value from the fixed-effects model.</li> <li><em>NEAREST_GENE</em> - the gene closest to the respective variant.</li> </ul> <p> </p>
Association mapping identified novel candidate loci affecting wood formation in Norway spruce
<p>Data sets associated with the study for the Association mapping and identification of novel candidate loci affecting wood formation in Norway spruce</p>
Quantitative Trait Loci of Solanaceae species
<p>This archive contains experimental data on Quantitative Trait Loci (QTLs) mapped in <em>Solanacea</em> species (tomato and potato). QTLs were extracted from scientific literature using the QTLTableMiner++ tool. The resulting data are distributed in:</p> <ul> <li><a href="https://sqlite.org/">SQLite</a> database files (.db)</li> <li>CSV files (.csv)</li> <li><a href="https://www.w3.org/TR/turtle/">RDF/</a><a href="https://www.w3.org/TR/turtle/">Turle</a> files (gzip-ed .ttl)</li> </ul>
Figure. PCA analysis based on GH-MspI, GH-AluI, PRL, and DGAT1 loci in Turkish native cattle breeds (Turkish Grey - TG, East Anatolian Red - EAR, Anatolian Black - AB, and South Anatolian Red - SAR). in Growth hormone (GH), prolactin (PRL), and diacylglycerol acyltransferase (DGAT1) gene polymorphisms in Turkish native cattle breeds
Figure. PCA analysis based on GH-MspI, GH-AluI, PRL, and DGAT1 loci in Turkish native cattle breeds (Turkish Grey - TG, East Anatolian Red - EAR, Anatolian Black - AB, and South Anatolian Red - SAR).
Fig. 1. Maximum likelihood tree generating from a 399 in Isolation and Characterization of Polymorphic Microsatellite Loci for Caridina cantonensis and Transferability Across Eight Confamilial Species (Atyidae, Decapoda)
Fig. 1. Maximum likelihood tree generating from a 399-bp long COI dataset (GenBank accession no. MH176649-MH176993). SH-alrt/ bootstrap support values are indicated at major nodes. Each coloured notation represents one species.
FIGURE 2 in Development of microsatellite loci and population genetics of the catfish Pimelodus yuma (Siluriformes: Pimelodidae)
FIGURE 2 | Discriminant analysis of principal components for nine microsatellite loci and 138 individuals of Pimelodus yuma in three sections (S4/5, S6 and S7/8) of the Cauca River.
FIGURE 1 in Development of microsatellite loci and population genetics of the catfish Pimelodus yuma (Siluriformes: Pimelodidae)
FIGURE 1 | Studied sampling sites of Pimelodus yuma along the lower sections (S4–S8) of the Cauca River. The pentagons indicate sampling sites in floodplain lakes and the stars indicate sites along the main channel of the river.
FIGURE 2 in Population genetics of the endangered catfish Pseudoplatystoma magdaleniatum (Siluriformes: Pimelodidae) based on species-specific microsatellite loci
FIGURE 2 | Results of Structure (A, B) and Discriminant analysis of principal components (C) for Pseudoplatystoma magdaleniatum. A: K = 1; B: K = 2; M: Margento, PC: Punta Cartagena, PB: Puerto Berrío, SN: Samaná Norte.
FIGURE 3 in Development of microsatellite loci and population genetics of the catfish Pimelodus yuma (Siluriformes: Pimelodidae)
FIGURE 3 | STRUCTURE results for Pimelodus yuma showing K= 2 genetic stocks in three sections (S4/5, S6 and S7/8) of the Cauca River.
Expression quantitative trait loci influence DNA damage-induced apoptosis in cancer
<p><strong>Exposure expression quantitative trait loci (e2QTL)</strong></p> <p>The analysis of e2QTL allows for the identification of context-specific eQTL effects (Kim-Hellmuth et al. (2017), PMID: 28814792). To evaluate how inter-individual genetic variability influences the regulation of DNA damage-induced apoptosis, we performed e2QTL analysis of CD8+ T cells from 461 healthy European participants stimulated with high doses of 5 different carcinogens. These include Methyl-methanesulfonate (MMS), tert-butyl-hydroperoxide (TBOOH), benzo(a)pyrene-7,8-diol-9,10-epoxide (BPDE), 4-hydroxycyclophosphamide (HC) and UVC radiation.</p> <p><code>eQTL_DNA_damage_induced_apoptosis.csv:</code> eQTL data. FastQTL was used to analyze cis-eQTL within a 1 MB window of a gene’s transcription start site. Filtering and normalization of expression data was performed as described by the Genotype Tissue Expression (GTEx) project (The GTEx Consortium (2015), PMID: 25954001) including 60 PEER factors, top 3 genotype PCs and sex as covariates. Genotypes were filtered by PHWE > 10-6 and MAF > 5 %. Adjusted p-values were generated using 1,000 to 10,000 permutations. Variant IDs (CHR:POS:REF:ALT) are based on GRCh38.</p> <p><code>e2QTL_DNA_damage_induced_apoptosis.csv:</code> e2QTL data. The most significant variant for each analyzed gene was determined based on eQTL data to calculate e2QTL in a z-test that were corrected for multiple testing using Bonferroni correction as described by Kim-Hellmuth et al. (2017). Variant IDs (CHR:POS:REF:ALT) are based on GRCh38.</p> <p> </p>
Linked collectors and determiners for: Fungal 18S Ribosomal RNA (SSU) RefSeq Targeted Loci Project.
Natural history specimen data linked to collectors and determiners held within, "Fungal 18S Ribosomal RNA (SSU) RefSeq Targeted Loci Project". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/3bfbda20-1a91-4cf9-992f-bc1e9e5b7dad">https://bionomia.net/dataset/3bfbda20-1a91-4cf9-992f-bc1e9e5b7dad</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/3bfbda20-1a91-4cf9-992f-bc1e9e5b7dad">https://gbif.org/dataset/3bfbda20-1a91-4cf9-992f-bc1e9e5b7dad</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Bacterial 16S Ribosomal RNA RefSeq Targeted Loci Project.
Natural history specimen data linked to collectors and determiners held within, "Bacterial 16S Ribosomal RNA RefSeq Targeted Loci Project". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/0b0dc293-3b26-49db-b9f1-817b31ebf603">https://bionomia.net/dataset/0b0dc293-3b26-49db-b9f1-817b31ebf603</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/0b0dc293-3b26-49db-b9f1-817b31ebf603">https://gbif.org/dataset/0b0dc293-3b26-49db-b9f1-817b31ebf603</a>. Formatted as a Frictionless Data package.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.