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1,283 results for “Copying”
Data from: Mining from transcriptomes: 315 single-copy orthologous genes concatenated for the phylogenetic analyses of Orchidaceae
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Data from: Distribution and functionality of copy number variation across European cattle populations
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Landmark data for copy-cat evolution: Divergence and Convergence within and between cat and dog breeds
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Data from: High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure
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Paternally inherited P-element copy number affects the magnitude of hybrid dysgenesis in Drosophila simulans and D. melanogaster
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Phylogeny and biogeography of Fagus (Fagaceae) based on 28 nuclear single/low‐copy loci
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Data from: Mate copying in Drosophila simulans
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IO Islamic 2412(2). Rauḍat-alṣafa. A Copy of Mîr-khwând's
<p>IO Islamic 2412(2). Rauḍat-alṣafa. A Copy of Mîr-khwând’s</p>
IO Islamic 2538. Wâḳi'ât-i-Bâbarî, A complete copy of the rare Ć'aghatâi or Turkî Bâbarnama
<p>IO Islamic 2538. Wâḳi’ât-i-Bâbarî, A complete copy of the rare Ć’aghatâi or Turkî Bâbarnama</p>
Table S1.- Occurrence analysis in alpha-proteobacteria, represented by number of copies of each gene on strain genome.
<p>Data set of 204 alphaproteobacteria to analyze for the presence and absence of 12 proteins related to the pantothenate synthesis and transport. The protein FASTA files (faa) for each of the genomes were downloaded from the RefSeq NCBI database. Protein sequences with an expectation value (E) of 10<sup>-3</sup>or less were considered as putative homologues. We used Proteinortho v5.15 to obtain the clusters of orthologous proteins from the 204 protein FASTA files. Next, we used the Pfam v31.0 database to determine which protein ortho clusters represent the 12 proteins of interest analyzed in this work. The proteins we searched for were: PYD1, PYD2, PYD3, GAD, KPHMT, PS, ADC, KPR, MRF, KAR, Aam and GabT.</p>
IO Islamic 127. Burhân-i-Maâthir, A Defective copy of 'Alî bin 'Azîz-allâh Ṭabâṭabâ's History of the Bahmanîs and Niżâmshâhîs of Gulbargah, Bîdar, and Aḥmadnagar
<p>IO Islamic 127. Burhân-i-Maâthir, A Defective copy of ‘Alî bin ‘Azîz-allâh Ṭabâṭabâ’s History of the Bahmanîs and Niżâmshâhîs of Gulbargah, Bîdar, and Aḥmadnagar</p>
IO Islamic 2927. Ta'rîkh-i-'âlamârâi-'abbâsî, A Complete Copy of Iskandar Munshî's History of Shâh 'Abbâs the Great
<p>IO Islamic 2927. Ta’rîkh-i-‘âlamârâi-‘abbâsî, A Complete Copy of Iskandar Munshî’s History of Shâh ‘Abbâs the Great</p>
IO Islamic 1493. Ta'rîkh-i-'âlamârâi-'abbâsî, A Complete Copy of Iskandar Munshî's History of Shâh 'Abbâs the Great
<p>IO Islamic 1493. Ta’rîkh-i-‘âlamârâi-‘abbâsî, A Complete Copy of Iskandar Munshî’s History of Shâh ‘Abbâs the Great</p>
IO Islamic 595. Jawâmi'-alḥikâyât wa lawâmi'-alriwâyât, A Complete Copy of the Famous Collection of Stories and Anecdotes
<p>IO Islamic 595. Jawâmi’-alḥikâyât wa lawâmi’-alriwâyât, A Complete Copy of the Famous Collection of Stories and Anecdotes</p>
IO Islamic 1385. Jawâmi'-alḥikâyât wa lawâmi'-alriwâyât, A Fragmentary Copy of the First ḳism of the Jawâmi'-alḥikâyât
<p>IO Islamic 1385. Jawâmi’-alḥikâyât wa lawâmi’-alriwâyât, A Fragmentary Copy of the First ḳism of the Jawâmi’-alḥikâyât</p>
Simulated data and results from "Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data"
<p>This dataset contains all the simulated data and the results of all the considered methods in the benchmark presented in "Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data" [Zaccaria & Raphael, 2018]. All the data in this dataset and the corresponding formats are fully described at <a href="https://github.com/raphael-group/hatchet-paper">https://github.com/raphael-group/hatchet-paper</a>. The folder <em>simulations</em> which contains the entire dataset has been compressed with standard <em>zip</em>.</p>
Copy Number variants in Mallotus villosus
<p>Taking advantage of recent developments allowing CNV analysis from RAD-seq data (<a class="nova-e-link nova-e-link--color-inherit nova-e-link--theme-decorated" href="https://www.researchgate.net/deref/http%3A%2F%2Fdx.doi.org%2F10.1111%2Fmec.15565?_sg%5B0%5D=-uwA9TZisRRXnspI5ElYUaPv2ChLuHLDZPIJZABoML2rc-geS2mVnZVIt2u4FAB6_SPD-DeRxtzyN3RjHivkmfmvEg.JqPMUYewJwfNoZvoALtl54UTEL4BWYI0NA87y3HrK16wm8cRVOG0c0owiV4QoaSysHfAZCLPkLmn-UaqCdolJQ">10.1111/mec.15565</a>), we investigated how variation in fitness-related traits, local environmental conditions and demographic history are associated with CNVs, and how subsequent copy number variation drives population genetic structure in a marine fish, the capelin (<i>Mallotus villosus</i>). We collected 1536 DNA samples from 35 sampling sites in the north Atlantic Ocean and identified 6620 putative CNVs. Raw sequencing data for GBS libraries have been published in a previous study (Cayuela et al. 2020, <a class="nova-e-link nova-e-link--color-inherit nova-e-link--theme-decorated" href="https://www.researchgate.net/deref/http%3A%2F%2Fdx.doi.org%2F10.1111%2Fmec.15499?_sg%5B0%5D=OGdqMkvPArx5ICrgLrdT_ifFufXzoOZp0J7gLQEctL4EWpJv-h9FK8yFaom_h68N368lpxVYXRREN9BRpAi7lH0n8A.ylPnOWuObAEr1NJn9bzfYxNNAAwvYDvN0jDBR05xnfdW8Azf-PmnI7jDZFhecO1Kt1aTdFuxG0Yr3ff2e10XCg">10.1111/mec.15499</a>) and are available under accession no. PRJNA631144. Here, we provide the files of normalized read depth for the 6620 putative CNVs and environmental data used in our CNV analyses.</p>
Koranic Science, a Copy of Kashshâf [IO Bijapur 280]
<ul> <li>al-Qurʼān القرآن الكريم</li> <li><strong>This manuscript is now IO Bijapur 280 in the India Office collections.</strong></li> <li><strong>[metadata:</strong><a href="https://de.wikipedia.org/wiki/Otto_Loth"> <strong>Otto Loth, </strong></a><strong><em><a href="http://doi.org/10.5281/zenodo.3923636">A Catalogue of the Arabic Manuscripts in the Library of the India Office</a></em>, (volume 1), no. 55 here with further notations and hyperlinks]</strong>.</li> </ul> <p>55.</p> <p>B 280. Size 11<sup>1/4</sup> in. by 8<sup>1/4</sup> in.; foll. 237. Thirty-one lines in a page.</p> <p>The First Part of the <em>Kashshâf</em>, imperfect both at the beginning and end. The first words are والکشف (=p. ٢١ Lees), and it ends with Sû. 8, 54.</p> <p>Written in two different hands. Coloured lines round the pages. Many illegible glosses in the first portion.</p> <p> </p>
Data from: Fluorescent protein-mediated colour polymorphism in reef corals: multi-copy genes extend the adaptation/acclimatization potential to variable light environments
The genomic framework that enables corals to adjust to unfavourable conditions is crucial for coral reef survival in a rapidly changing climate. We have explored the striking intraspecific variability in the expression of coral pigments from the green fluorescent protein (GFP) family to elucidate the genomic basis for the plasticity of stress responses among reef corals. We show that multi-copy genes can greatly increase the dynamic range over which corals can modulate transcript levels in response to the light environment. Using the red fluorescent protein amilFP597 in the coral Acropora millepora as a model, we demonstrate that its expression increases with light intensity, but both the minimal and maximal gene transcript levels vary markedly among colour morphs. The pigment concentration in the tissue of different morphs is strongly correlated with the number of gene copies with a particular promoter type. These findings indicate that colour polymorphism in reef corals can be caused by the environmentally regulated expression of multi-copy genes. High-level expression of amilFP597 is correlated with reduced photodamage of zooxanthellae under acute light stress, supporting a photoprotective function of this pigment. The cluster of light-regulated pigment genes can enable corals to invest either in expensive high-level pigmentation, offering benefits under light stress, or to rely on low tissue pigment concentrations and use the conserved resources for other purposes, which is preferable in less light-exposed environments. The genomic framework described here allows corals to pursue different strategies to succeed in habitats with highly variable light stress levels. In summary, our results suggest that the intraspecific plasticity of reef corals' stress responses is larger than previously thought.
Data from: Gene copy number variations as signatures of adaptive evolution in the parthenogenetic, plant-parasitic nematode Meloidogyne incognita
Adaptation to changing environmental conditions represents a challenge to parthenogenetic organisms and until now, how phenotypic variants are generated in clones in response to the selection pressure of their environment remains poorly known. The obligatory parthenogenetic root-knot nematode species Meloidogyne incognita has a worldwide distribution and is the most devastating plant-parasitic nematode. Despite its asexual reproduction, this species exhibits an unexpected capacity of adaptation to environmental constraints, e.g., resistant hosts. Here we used a genome-wide comparative hybridization strategy to evaluate variations in gene copy numbers between genotypes of M. incognita resulting from two parallel experimental evolution assays on a susceptible vs. resistant host plant. We detected gene copy number variations (CNVs) associated with the ability of the nematodes to overcome resistance of the host plant, and this genetic variation may reflect an adaptive response to host resistance in this parthenogenetic species. The CNV distribution throughout the nematode genome is not random and suggests the occurrence of genomic regions more prone to undergo duplications and losses in response to the selection pressure of the host resistance. Furthermore, our analysis revealed an outstanding level of gene loss events in nematode genotypes that have overcome the resistance. Overall, our results support the view that gene loss could be a common class of adaptive genetic mechanism in response to a challenging new biotic environment in clonal animals.
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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)
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.