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15,277 results for “GENETICS”
FIGURE 5 in A new species of Ducetia (Tettigoniidae, Phaneropterinae) from Mindanao, Philippines based on bioacoustics, stridulatory file morphology and genetic data
FIGURE 5. Tooth distribution on the stridulatory file of Ducetia laniae sp. nov. ♂ based on tooth length (A) and inter-tooth distance (B).
FIGURE 6 in A new species of Ducetia (Tettigoniidae, Phaneropterinae) from Mindanao, Philippines based on bioacoustics, stridulatory file morphology and genetic data
FIGURE 6. Ducetia laniae sp. nov. ♀: habitus in lateral (A) and dorsal (B) views; head, pronotum and anterior part of tegmina in dorsal view (C); abdominal apex in lateral (D) and ventral (E) views. Scale bars: 5 mm (A, B); 2 mm (C–E).
FIGURE 4 in A new species of Ducetia (Tettigoniidae, Phaneropterinae) from Mindanao, Philippines based on bioacoustics, stridulatory file morphology and genetic data
FIGURE 4. Ducetia laniae sp. nov. ♂: head, pronotum and anterior part of tegmina in dorsal view (A); face in anterior view (B); head, pronotum and anterior part of tegmina in lateral view (C); stridulatory file of the left tegmen in ventral view (D); abdominal apex in lateral (E) and ventral (F) views. Scale bars: 2 mm (A, C, E, F); 1 mm (B, D).
Data and Code for "Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic"
<p>Please see the README.md file for a detailed description of each of the code and data files in this dataset.</p>
Summary Statistics for Genetic determinants and phenotypic consequences of blood T-cell proportions in 207,000 diverse individuals
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Genetic alterations and expression programs of oral squamous cell carcinoma associated with betel quid chewing
<p><span>Betel quid (BQ) chewing is a profound risk for</span><span> oral squamous cell carcinoma (OSCC) <span>in Southeast Asia.</span> To decipher contributory genomic abnormalities and transcriptional reprogramming in these malignancies, we conducted a multi-omics survey, including exome sequencing of tumor-normal pairs from <span>261 male </span>patients with OSCC (129 habitual BQ chewers and 132 non-BQ users), alone with integrated single-cell and spatial transcriptomics of a set of tumors. Comparative analyses of the mutational catalog identified enrichment of significantly altered genes (e.g mutations of <em>TP53</em> and <em>CHUK</em>, copy gains of <em>MAP3K13</em> and <em>FADD</em>, copy losses of <em>CDKN2A</em>) and mutational signatures associated with BQ chewing. Assessment of oncogenic and co-occurring actionable alterations demonstrated frequently altered oncogenic pathways (Hippo and p53 signaling) and potential combination therapy opportunities linked to BQ use. In addition, evaluation of epithelial, immune, stromal expression programs in the corresponding tissue compartments revealed a shift of tumor microenvironment in BQ-related OSCC, characterized by induced hypoxia of tumor epithelium, altered immunosuppression of dendritic cells, and raised sprouting angiogenesis of tumor endothelium. Quantitative predictions of intercellular communications inferred a more heterogeneous cell-cell crosstalk among BQ-related OSCC, highlighted by extensive interactions of fibroblasts and dendritic cells with other non-epithelial cell types via mostly extracellular matrix-receptor signaling pathways. Collectively, these differences in genomic landscape and tumor niche suggest that OSCC caused by BQ chewing could be an etiological subtype different from their BQ-negative counterparts.</span></p>
Non-linear genetic regulation of the blood plasma proteome - GWAS Summary Statistics
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Quantitative genetics of eggshell colouration
<p>Exploring the evolutionary architecture of female sexual traits and their potential evolvability is important to understand their possible role as post-mating sexual signals. Egg colouration has been proposed to be one of these post-mating sexual signals, honestly advertising female quality in birds, especially in blue-green laying species. In this study, we used an animal model in a Bayesian framework to estimate the evolvability of multiple descriptors of blue-green egg colouration and egg size in a wild long-term monitored population of spotless starlings (<em>Sturnus unicolor</em>). Our results show low to moderate heritability (<em>h</em><sup>2 </sup>= 0.31 – 0.44) for three egg colour descriptors (blue-green chroma, chroma and lightness) and egg size. Using the coefficient of additive genetic variance (<em>CV</em><sub>A</sub>) and the evolvability (<em>I</em><sub>A</sub>) as proxies of evolutionary potential of all components of this trait, we found low values of <em>C</em><em>V</em><sub>A</sub> for all these variables, suggesting a small evolutionary potential of these phenotypic traits, contrasting to previous results reported in another blue-green egg laying species. Our results indicate a modest raw genetic material of this trait on which sexual selection can act upon and, therefore, a small probability for these traits to respond easily to selection.</p>
Paternal lineages and genetic diversity in Holstein-Friesian cattle
<p>This database contains paternal lineages and genetic diversity data in Holstein-Friesian cattle (1950-2021).</p>
Genetic datasets, climatic conditions at sampled localities, and occurrence data to: Ice age-driven range shifts of diploids and expanding autotetraploids within a conserved niche (Grünig, Patsiou & Parisod, 2024, New Phytologist)
<div> <h3><strong>This repository includes</strong></h3> - An overview of the raw sequencing reads deposited in the European Nucleotide Archive (ENA) for the 370 individuals sampled in 17 diploid and 19 tetraploid field populations <div>- Scripts used to genotype diploids and autotetraploids samples of <em>Biscutella laevigata</em> from ddRADseq data</div> <div>- Input data (as vcf format) used in population genetic analyses</div> <div>- Scripts used to run the different genetic analyses</div> <div>- Dataset of extracted climatic conditions at sampled localities</div> <div>- Occurrence dataset used for the climatic niche modelling</div> <br> <h3><strong>Description of the data and file structure</strong></h3> <strong>00.ENA_samples_correspondance.txt: </strong>provides ENA project ID, run ID (i.e. raw fastq files), sample ID, and alias for each sample included in the study.<br> <div> </div> <div><strong>1.scripts_reads_to_vcf.zip:</strong> consists of the following:</div> - <strong>1.reads_to_vcf.md: </strong>md file with scripts documenting the read quality check, demultiplexing, mapping, SNP calling using GATK4, and filtering steps<br> <div>- Additional scripts called within <strong>1.reads_to_vcf.md</strong>:</div> <div>-- 1.3. Mapping: <strong>02_run_mapping_XXX.py</strong> and <strong>BWA-mem_bisc1_sg.py</strong> scripts</div> <div>-- 1.4.a. HaplotypeCaller: <strong>03_V1_gvcf.py</strong></div> <div>-- 1.4.b. GDBI + genotypeGVCF: <strong>03_V3_gdbi_genotype_per100scaf.py</strong></div> <br> <div><strong>2.datasets_genetics.tar.gz</strong> consists of the following</div> <br> <div>- <strong>bisc_all370_diminDP15_tetraminDP30.vcf.gz</strong>: "Initial SNPs dataset" = biallelic SNPs fulfilling GATK quality hard filtering recommendations, present in at least 50% of samples. Genotypes with DP<15 for diploids and DP<30 for tetraploids are set to no-call. This vcf was used as basis for fastsimcoal dataset preparation, and as basis for subsequent selection of loci fulfilling requirements of each analysis. It includes 2246701 biallelic SNPs for 370 samples</div> <br> <div>- <strong>bisc_all370_diminDP15_tetraminDP30_MD05_pruned.vcf.gz:</strong> subset of the "Initial SNPs dataset" retaining SNPs called in at least 50% of samples, and pruned for Linkage disequilibrium. This vcf includes 107574 biallelic SNPs for 370 samples and was used in the analysis of the proportion of diploids diagnostic alleles shared by tetraploids.</div> <br> <div>- <strong>bisc_all370_diminDP15_tetraminDP30_MD01_pruned.vcf.gz: </strong>subset of the "Initial SNPs dataset", retaining SNPs called in at least 90% of samples, and pruned for Linkage disequilibrium. This vcf includes 4444 biallelic SNPs for 370 samples and was used in the analyses of Population diversity and differentiation (SpaGeDi, GenoDive, PCA), and f3-statistics.</div> <br> <div>- <strong>bisc_all370_diminDP15_tetraminDP30_MD0.1_pruned_MAC3rm.vcf.gz:</strong> subset of the "Initial SNPs dataset", retaining SNPs called in at least 90% of samples, pruned for Linkage disequilibrium, and with a minor allele count of 3. This vcf includes 2593 biallelic SNPs for 370 samples and was used in STRUCTURE analysis</div> <br><br> <div><strong>3.pres_2x.txt:</strong> list of the 128 diploid occurrences used in climatic niche modelling</div> <br> <div><strong>3.pres_4x_strat_reg.txt:</strong> list of the 924 tetraploid occurrences used in climatic niche modelling</div> <br> <div><strong>biscall_chelsa_ordered_noDEM.txt:</strong> climatic data extracted from the CHELSA dataset at sampled localities</div> <br> <div><strong>4.plot_GTfreqs.md:</strong> markdown file including scripts to plot allele and genotype frequencies</div> <br> <div> </div> <h3><strong>Sharing/Access information</strong></h3> Raw sequencing reads have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under the accession number PRJEB48869:<a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB48869"> https://www.ebi.ac.uk/ena/browser/view/PRJEB48869</a></div>
Methodological approaches to assessing the genetic predisposition of Osteochondrosis of the tarsocrural joint in the Pura Raza Española horses
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Figs 1–2 in Molecular genetic confirmation of the subspecies status of blues Agriades orbitulus pheretimus (Staudinger, 1892) and A. orbitulus jugnei Churkin, 2004 (Lepidoptera: Lycaenidae: Polyommatinae)
Figs 1–2. Agriades orbitulus ssp.: ML-cladogram for DNA sequences: 1 — COI; 2 — ITS2. Рис. 1–2. Agriades orbitulus ssp.: ML-кладограмма длЯ ДНК сиквенсов: 1 — COI; 2 — ITS2.
Fig. 5 in Two evolutionary units on the South American razor clam Ensis macha (Bivalvia: Pharidae): genetic and morphometric evidence
Fig. 5 UPGMA dendrogram showing the relationships between shell shapes of the different localities and clades. The cut-off criterion (p <0.05) obtained with the MDGC test is indicated with a horizontal dashed line. See Fig. 1 for localities reference labels
Fig. 4 in Two evolutionary units on the South American razor clam Ensis macha (Bivalvia: Pharidae): genetic and morphometric evidence
Fig. 4 Plot of the first three principal components (PC) based on 57 Fourier coefficients from shell outlines of E. macha, along with the shapes of the reconstructed extremes (mean – 2SD, and mean + 2SD) configurations. Percentages of explained variance for each axis are in
Fig. 3 in Two evolutionary units on the South American razor clam Ensis macha (Bivalvia: Pharidae): genetic and morphometric evidence
Fig. 3 Boxplot of interspecific and intraspecific nuclear genetic distances of the two putatively different Ensis species
Fig. 1 in Two evolutionary units on the South American razor clam Ensis macha (Bivalvia: Pharidae): genetic and morphometric evidence
Fig. 1 Map of southern South America showing sampling localities (blue circles: Southern clade, green circles: Northern clade, and yellow triangles: oldest fossil records). Codes for the localities: ES (El Sótano, 40° 53′ S); PP (Punta Pozo, 41° 34′ S); PL (Puerto Lobos, 42° 00′ S); LT (La Tapera, 42° 21′ S); CC (Caleta Carolina, 44° 54′ S); B (Playa Bonita, 46° 00′ S); PB (Punta Buque, 48° 02′ S); ML (Monte León, 50° 19′ S); U (Puerto Almanza, Beagle Channel, 54° 52′ S); EP (El Porvenir, 53° 24′ S); An (Ancud, 41° 52′ S); N (Niebla, 39° 48′ S, Valdivia); Di (Dichato, 36° 37′ S); and Tr (Trujillo, 08° 06′ S). Light blue rectangles show the limit between biogeographical provinces: Argentina Province; Magellanic Province, and Intermediate Area. Orange stars correspond to the sampling localities of nuclear genomic data and the green rectangular bar indicates the geographical distribution of E. macha
FIGURE 5 in A new species of Homatula from the Red River drainage in Yunnan based on morphological and genetic data (Teleostei: Nemacheilidae)
FIGURE 5. Scatter plots of the first and second (left) and second and third (right) principal components (PCs) of pooled morphometrics data of tYpe specimens of Homatula coccinocola (n=5, 51.1–99.6 mm SL, solid circles) and H. change (n=18, 40.2–107.6 mm SL, hollow circles).
FIGURE 1. Homatula coccinocola, KIZ 2011002847 in A new species of Homatula from the Red River drainage in Yunnan based on morphological and genetic data (Teleostei: Nemacheilidae)
FIGURE 1. Homatula coccinocola, KIZ 2011002847, holotYpe, 99.6 mm SL; Yunnan: Honghe; Tengtiaojiang River.
FIGURE 9 in Diversity of Tropidurus (Squamata: Tropiduridae) in Paraguay-an integrative taxonomic approach based on morphological and molecular genetic evidence
FIGURE 9. Dextral lateral views of specimens of T. catalanensis (A, SMF 100093) indicating inguinal (left arrow) and axillary (right arrow) folds, compared with T. etheridgei (B, SMF 87389), which lacks these folds.
FIGURE 8 in Diversity of Tropidurus (Squamata: Tropiduridae) in Paraguay-an integrative taxonomic approach based on morphological and molecular genetic evidence
FIGURE 8. Differences in the mucronation of dorsal scales of Tropidurus catalanensis (above, SMF 100091) and T. torquatus (below, SMF 100097).
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.