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15,277 results for “GENETICS”
Link to Dataset related to article "Interpreting Non-coding Genetic Variation in Multiple Sclerosis Genome-Wide Associated Regions"
<p>Link to Dataset related to article "Interpreting Non-coding Genetic Variation in Multiple Sclerosis Genome-Wide Associated Regions"</p> <p>Multiple sclerosis (MS) is the most common neurological disorder in young adults. Despite extensive studies, only a fraction of MS heritability has been explained, with association studies focusing primarily on protein-coding genes, essentially for the difficulty of interpreting non-coding features. However, non-coding RNAs (ncRNAs) and functional elements, such as super-enhancers (SE), are crucial regulators of many pathways and cellular mechanisms, and they have been implicated in a growing number of diseases. In this work, we searched for possible enrichments in non-coding elements at MS genome-wide associated loci, with the aim to highlight their possible involvement in the susceptibility to the disease. We first reconstructed the linkage disequilibrium (LD) structure of the Italian population using data of 727,478 single-nucleotide polymorphisms (SNPs) from 1,668 healthy individuals. The genomic coordinates of the obtained LD blocks were intersected with those of the top hits identified in previously published MS genome-wide association studies (GWAS). By a bootstrapping approach, we hence demonstrated a striking enrichment of non-coding elements, especially of circular RNAs (circRNAs) mapping in the 73 LD blocks harboring MS-associated SNPs. In particular, we found a total of 482 circRNAs (annotated in publicly available databases) vs. a mean of 194 ± 65 in the random sets of LD blocks, using 1,000 iterations. As a proof of concept of a possible functional relevance of this observation, we experimentally verified that the expression levels of a circRNA derived from an MS-associated locus, i.e., hsa_circ_0043813 from the <em>STAT3</em> gene, can be modulated by the three genotypes at the disease-associated SNP. Finally, by evaluating RNA-seq data of two cell lines, SH-SY5Y and Jurkat cells, representing tissues relevant for MS, we identified 18 (two novel) circRNAs derived from MS-associated genes. In conclusion, this work showed for the first time that MS-GWAS top hits map in LD blocks enriched in circRNAs, suggesting circRNAs as possible novel contributors to the disease pathogenesis.</p> <p>GEO database</p> <p>URL: <a href="https://www.ncbi.nlm.nih.gov/geo/">https://www.ncbi.nlm.nih.gov/geo/</a></p> <p>Numero di accesso del dataset: GSE110525</p>
Datasets for "Intraspecific interactions in the annual legume Medicago minima are shaped by both genetic variation for competitive ability and reduced competition among kin"
<p>Datasets for “Intraspecific interactions in the annual legume <em>Medicago minima</em> are shaped by both genetic variation for competitive ability and reduced competition among kin”</p> <p>Two datasets are provided.</p> <p>root_behavior_experiment_for_ms.csv: provides data relative to a root behaviour experiment where <em>Medicago minima</em> genotypes grew either with a kin or a non kin. Direction of root growth, root length and biomass were measured.</p> <p>Medicago_minima_biomass_dataMerge.csv: provides data relative to a minicommunity experiment where <em>Medicago minima </em>genotypes were grown surrounded by three kin genotypes, or three non-kin genotypes (i.e. stranger to the central plant but identical to each other) or three stranger genotypes (stranger to the central plant and to each other). For this second experiment above-ground growth and biomass were monitored.</p> <p>Detailed information on the dataset variables are provided in the metadata file.</p> <p>Code for data wrangling and analyses is included in the manuscript as an appendix.</p>
Dataset for the article: "Weak genetic structure despite strong genomic signal in lesser sandeel in the North Sea"
<p>Dataset used for the article: "Weak genetic structure despite strong genomic signal in lesser sandeel in the North Sea".</p> <p>Dataset consists on a VCF file from 471 individuals of lesser sandeel, <em>Ammodytes marinus</em> (L.). This VCF is the end product of the bioinformatic analysis described in the paper Jimenez-Mena et al. (2019). Data was obtained from double-digest Restriction-site Associated DNA (ddRAD) sequencing. More information can be obtained in Methods of the article. The information of each of the individuals in the VCF is also included as a separate file, as well as the supplementary tables of the article.</p>
data for the PCI publication "New insights into the population genetics of partially clonal organisms: when seagrass data meet theoretical expectations"
<p><strong>Data analyzed int he article "New insights into the population genetics of partially clonal organisms: when seagrass data meet theoretical expectations", doi </strong> <a href="https://arxiv.org/abs/1902.10240v5">https://arxiv.org/abs/1902.10240v5</a> <strong> doi of the PCI recommandation: </strong>https://doi.org/10.24072/pci.evolbiol.100083</p>
Fig. 2 in Genetic divergence of a newly documented population of the cecidogenous micromoth Eugnosta azapaensis Vargas & Moreira (Lepidoptera: Tortricidae) in the Atacama Desert of northern Chile
Fig. 2. Median joining network of the haplotypes of the DNA barcode fragment (658 bp) of the cytochrome c oxidase subunit I (COI) gene of Eugnosta azapaensis from Azapa (white) and Chaca (black) valleys, Atacama Desert of northern Chile. H1, H2, H3, H4 haplotypes; circles proportional to the frequency of the respective haplotype; numbers between circles indicates variable sites; gray triangle a median vector.
Fig. 1 in Genetic divergence of a newly documented population of the cecidogenous micromoth Eugnosta azapaensis Vargas & Moreira (Lepidoptera: Tortricidae) in the Atacama Desert of northern Chile
Fig. 1. The study area in South America (left) and the sampling sites (right) of Eugnosta azapaensis in the Atacama Desert of northern Chile. The type locality Azapa Valley (black circle) and the newly documented locality Chaca Valley (black triangle).
Figure 4 in Genetic lineages of Parisotoma notabilis sensu lato (Collembola) in Eastern Europe and the Caucasus
Figure 4. Sites of lineage findings in the Caucasus region and in southern Eastern Europe (L0, L1, L2, L3, L4-Hebert, L-Hyrcan, L-Crimea, L-Cheget, L-Georgia, L-Khosta).
Figure 1 in Genetic lineages of Parisotoma notabilis sensu lato (Collembola) in Eastern Europe and the Caucasus
Figure 1. Maximum Likelihood genetic tree of 10 lineages of P. notabilis based on the COI gene fragment.
Figure 6 in Genetic divergences of South and Southeast Asian frogs: a case study of several taxa based on 16S ribosomal RNA gene data with notes on the generic name Fejervarya
Figure 6. Maximum likelihood (ML) tree of bufonid frogs based on nucleotide sequences of the mitochondrial 16S rRNA gene with Leptophryne borbonica as an outgroup. The bootstrap support (>50%) is indicated at nodes in the order of ML (500) replicates. Asterisks represent Bayesian posterior probability (BPP; * ≥95%). Specimens examined in this study are indicated by boldface type.
Figure 2 in Genetic divergences of South and Southeast Asian frogs: a case study of several taxa based on 16S ribosomal RNA gene data with notes on the generic name Fejervarya
Figure 2. Maximum likelihood (ML) tree based on nucleotide sequences of the mitochondrial 16S rRNA gene from 88 haplotypes of frogs (Table 1), with Xenopus laevis as an outgroup. Bootstrap support (>50%) is indicated at nodes in the order of ML (1000) replicates. Asterisks represent Bayesian posterior probability (BPP; * ≥95%).
Figs. 7–11 in New morphological and genetic data of Gigantorhynchus echinodiscus (Diesing, 1851) (Acanthocephala: Archiacanthocephala) in the giant anteater Myrmecophaga tridactyla Linnaeus, 1758 (Pilosa: Myrmecophagidae)
Figs. 7–11. Light microscopy of adult Gigantorhynchus echinodiscus from Mymercophaga tridactyla. 7. Proboscis with a crown of large hooks in the apex and small hooks, and a proboscis receptacle (Re); 8. Trunk with pseudo segmentation (arrows) and the end of the lemnisci (Le); 9. Male reproduction organs, testis (Te), cement glands in pair (Cgl), ejaculatory duct (Ed); 10. Detail of the posterior end of adult female showing the uterus (Ut), vagina (Va, arrow) and gonopore subterminal (Gp); 11. Egg ellipsoid showing the outer membrane thick (Om), inner membrane (Im) thin, embryo (Em).
Figs.1–6 in New morphological and genetic data of Gigantorhynchus echinodiscus (Diesing, 1851) (Acanthocephala: Archiacanthocephala) in the giant anteater Myrmecophaga tridactyla Linnaeus, 1758 (Pilosa: Myrmecophagidae)
Figs.1–6. Line drawing of Gigantorhynchus echinodiscus from Mymercophaga tridactyla. 1. Praesoma with the proboscis presenting a crown with robust hooks followed by small hooks, a receptacle proboscis, and papillae in the base of the neck; 2. Three different robust hooks in the crown and a one small type in the proboscis; 3. Unsegmented anterior part of the trunk, and lemnisci filiform reaching the middle region of the trunk; 4. Posterior region of adult male showing reproductive organs; 5. Posterior region of adult female showing the uterus, vagina and gonopore subterminal; 6. Egg.
Fig. 12–17 in New morphological and genetic data of Gigantorhynchus echinodiscus (Diesing, 1851) (Acanthocephala: Archiacanthocephala) in the giant anteater Myrmecophaga tridactyla Linnaeus, 1758 (Pilosa: Myrmecophagidae)
Fig. 12–17. Scanning electron micrographs of adult Gigantorhynchus echinodiscus from Mymercophaga tridactyla. 12 and 13. Cylindrical proboscis armed with hooks (Ho) showing a space (Sp) between the two circles of large hooks and small rootless spines, neck (Ne), trunk (Tr), lateral papillae (Pa, arrowhead); 14. Detail of the crown with two circles of large hooks (arrow – 1st row and asterisk – 2nd row); 15. Detail of the lateral papillae; 16 and 17. Posterior end of adult male showing the region without pseudo-segmentation (cross) and a copulatory bursa protruding from the body (CB).
Fig. 2 in Quantitative genetics of gastrointestinal strongyle burden and associated body condition in feral horses
Fig. 2. Predicted relationship between an individual's annual location and a) faecal egg count (measured as the natural logarithm of eggs per gram (EPG) + 25) and b) body condition. Location is scaled to a mean of 0 and standard deviation of 1, therefore 0 represents the centre of the island with −2 at the far west and 2 at the far east. The fitted line comes from the full univariate animal model in each case. In both cases, overlap between points is represented by darker point colour. In 2b. points have been jittered along the y axis to ease visualisation.
Fig. 2 in Genetic and morphological differentiation among populations of the narrowly endemic and karst forest-adapted Pilea pteridophylla (Urticaceae)
Fig. 2 Morphological variation among individuals of Pilea pteridophylla sampled along its distribution range in the tropical karst forest of southern Mexico. Plot of individual scores for the first two components of the principal component analysis using morphological data. Coloured symbols represent the two populations recognized for the species: red circles, Tabasco; and blue circles, Chiapas. Ellipses correspond to the 95% confidence intervals estimated for each population. The lines represent the dispersion of the individuals within each population
Fig. 3 in Genetic and morphological differentiation among populations of the narrowly endemic and karst forest-adapted Pilea pteridophylla (Urticaceae)
Fig. 3 Statistical parsimony networks of rps16-trnQ, trnL-trnF and rps16-trnQ + trnL-trnF dataset using the gaps as missing data. Coloured symbols represent the two populations recognized for the species: red circles, Tabasco; and blue circles, Chiapas. Open-white circles represent the number of mutational steps between haplotypes. The size of the circles is proportional to the frequency of each haplo-
Fig. 1 in Genetic and morphological differentiation among populations of the narrowly endemic and karst forest-adapted Pilea pteridophylla (Urticaceae)
Fig. 1 Mountain karst forests of Mexico and the studied species Pilea pteridophylla A. K. Monro (Urticaceae). A Geographic distribution of the Mountain karst forests of Mexico. B Individual from the Chiapas population. C Individual from the Tabasco population
Text-fig. 4. Electrophoresis after amplification: Electrophoretical analysis of mitochondrial DNA. mtDNA sequences were amplified by primers F15.412 and R16.169 (450 bp), R16.269 (550 bp), R16.519 (800 bp). Lane 1 are primers F15.412 + R16.169, lane 2 primers F15.412 + R16.269, lane 3 primers F15.412 + R16.519, NC – negative control – water, L – 100 bp DNA ladder (band size from 100 bp to 1500 bp). in Genetic Analysis Of Possibly The Oldest Greyhound Remains Within The Territory Of The Czech Republic As Proof Of A Local Elite Presence At Chotěbuz-Podobora Hillfort In The 8 -9 Century Ad
Text-fig. 4. Electrophoresis after amplification: Electrophoretical analysis of mitochondrial DNA. mtDNA sequences were amplified by primers F15.412 and R16.169 (450 bp), R16.269 (550 bp), R16.519 (800 bp). Lane 1 are primers F15.412 + R16.169, lane 2 primers F15.412 + R16.269, lane 3 primers F15.412 + R16.519, NC – negative control – water, L – 100 bp DNA ladder (band size from 100 bp to 1500 bp).
Text-fig. 1. Bottom view of the spoke bone of the excavated greyhound-like dog (above) and the spoke bone of a dog of the same size category (below). The gracility of the spoke bone of the greyhound-like dog is clearly visible. Photo by D. Nývlt. in Genetic Analysis Of Possibly The Oldest Greyhound Remains Within The Territory Of The Czech Republic As Proof Of A Local Elite Presence At Chotěbuz-Podobora Hillfort In The 8 -9 Century Ad
Text-fig. 1. Bottom view of the spoke bone of the excavated greyhound-like dog (above) and the spoke bone of a dog of the same size category (below). The gracility of the spoke bone of the greyhound-like dog is clearly visible. Photo by D. Nývlt.
Text-fig. 5. Multiple sequence alignment of mtDNA from ancient bone and recent greyhound, (Gundry et al. 2007) primer pair A – F15.719 and R16.114. in Genetic Analysis Of Possibly The Oldest Greyhound Remains Within The Territory Of The Czech Republic As Proof Of A Local Elite Presence At Chotěbuz-Podobora Hillfort In The 8 -9 Century Ad
Text-fig. 5. Multiple sequence alignment of mtDNA from ancient bone and recent greyhound, (Gundry et al. 2007) primer pair A – F15.719 and R16.114.
ScienceDex guides
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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.