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200 results for “Genomic Resources”
Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life
<p>For each ancestral gene, we assign a stable identifier, and provide additional information designed to facilitate analysis: an inferred name (based on its descendants in extant genomes), a reconstructed protein sequence, a set of inferred Gene Ontology (GO) annotations, and a “proxy gene” for each ancestral gene, defined as the least-diverged descendant of the ancestral gene in a given extant genome.</p>
Efficient Real-Time Selective Genome Sequencing on Resource-Constrained Devices
<p>This dataset contains the curated nanopore raw signal data in <a href="https://www.nature.com/articles/s41587-021-01147-4">BLOW5 format </a>used to benchmark <a href="https://github.com/beebdev/HARU/">Hardware Accelerated Read Until (HARU)</a>. This dataset was created by using the publicly available datasets: <a href="https://community.artic.network/t/links-to-raw-fast5-fastq-data-for-artic-protocol/17">SARS-CoV-2 SP1</a> (1.382M reads) and <a href="https://ncbi.nlm.nih.gov/sra/SRX11368475">NA12878 PromethION subset</a> (500,000 reads). The tarball when extracted will have the following directory structure:</p> <p>haru-data<br> ├── na12878-rfc1<br> │ ├── blow5-rawsignal<br> │ │ ├── na12878_dna_0.blow5<br> │ │ ├── na12878_dna_100.blow5<br> │ │ ├── na12878_dna_101.blow5<br> │ │ ├── na12878_dna_102.blow5<br> │ │ ├── ...<br> │ └── reference<br> │ └── rfc1.fa<br> └── SARS-CoV-2-sp1<br> ├── blow5-rawsignal<br> │ ├── readgroup0<br> │ │ ├── reads_0_0.blow5<br> │ │ ├── reads_0_10.blow5<br> │ │ ├── reads_0_11.blow5<br> │ │ ├── reads_0_12.blow5<br> │ │ ├── ...<br> │ └── readgroup1<br> │ ├── reads_1_0.blow5<br> │ ├── reads_1_10.blow5<br> │ ├── reads_1_11.blow5<br> │ ├── ....<br> └── reference<br> └── nCoV-2019.reference.fasta</p> <p>nCoV-2019.reference.fasta is the SARS-CoV-2 MN908947.3 reference genome. rfc1.fa is the genomic region hr4:39262456-39391375 extracted from hg38 human genome. </p> <p> </p> <p> </p>
The Genomic Reference Resource for African Cattle: genome sequences and high-density array variants.
<p><em>The diversity in genome resources is fundamental to designing genomic strategies for local breed improvement and utilisation. These resources also support gene discovery and enhance our understanding of the mechanisms of resilience with applications beyond local breeds. We report here the genome sequences of 573 samples (198 new genomes) and high-density (HD) array genotyping of 1,082 samples (537 new samples) from indigenous African cattle populations. The new sequences have an average genome coverage of ~30X, three times higher than the average (~10X) of the over 300 sequences already in the public domain. Following variant quality checks, we identified approximately 32.4 million sequence variants and 661,943 HD autosomal variants mapped to the Bos taurus reference genome (ARS-UCD1.2). The new datasets were generated as part of the Centre for Tropical Livestock Genetic and Health (CTLGH) Genomic Reference Resource for African Cattle (GRRFAC) initiative, which aspires to facilitate the generation of this livestock resource. We hope this resource will be utilised by the global scientific community and breeders for sustainable global livestock improvement.</em></p>
Reference genome resources associated with the project: Functional genetic diversity is correlated with intensity of genetic drift in populations of an endangered rattlesnake
<p class="MsoNormal">Theory predicts that genetic erosion in small, isolated populations of endangered species can be assessed using estimates of neutral genetic variation reflecting long-term impacts of genetic drift, yet this widely used approach has been questioned in the genomics era. Here we leverage a chromosome-level assembly and whole genome resequencing data (N=110 individuals) from an endangered rattlesnake (<em>Sistrurus catenatus</em>) to evaluate the relationship between genome-wide neutral and functional diversity over long- and short-term timescales. As predicted for populations at long-term equilibrium, we found a positive correlation between population-level estimates of neutral genetic diversity (π) and the mean number of highly detrimental loss-of-function mutations, and a negative relationship between neutral genetic diversity and an estimate of genetic load. In contrast, we found only a weak, non-significant positive correlation between levels of neutral and adaptive variation. Additional analyses using estimates of drift at more recent time scales (> 100 generations) show expected correlations between both measures of genetic load, but a lack of a significant correlation with levels of adaptive variation. Individual-based demographic metrics that capture drift impacts over recent time scales confirm these results. Broadly, our results confirm that estimates of diversity and demography based on neutral genetic variation provide an accurate measure of a key component of genetic erosion – genetic load – in populations of a threatened vertebrate. Our findings also provide nuance to the neutral-functional diversity controversy by demonstrating that neutral genetic diversity is useful in predicting some, but not all, components of functional genetic diversity.</p>
Data from: "Transcriptome resources for two non-model freshwater crustacean species" in Genomic Resources Notes accepted 1 October 2014 to 30 November 2014
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Data from: "Discovery and characterization of 80 SNPs and 1,624 SSRs in the transcriptome of Atlantic mackerel (Scomber scombrus, L)" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015
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Microsatellite exploration in the climbing hydrangea (Hydrangea petiolaris Siebold & Zucc.) transcriptome: A resource for population genetics and functional genomics
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Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment
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Data from: "Transcriptome sequencing of the Antarctic Colobanthus quitensis (Kunth) Bartl (Caryophillaceae)" in Genomic Resources Notes Accepted 1 February 2015 – 31 March 2015
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Data from: A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans
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Supporting data for: The de novo genome of the Black-necked Snakefly (Venustoraphidia nigricollis Albarda, 1891): A resource to study the evolution of living fossils
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Chromosome-level genome of the peach fruit moth Carposina sasakii (Lepidoptera: Carposinidae) provides a resource for evolutionary studies on moths
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Reference genome resources associated with the project: Functional genetic diversity is correlated with intensity of genetic drift in populations of an endangered rattlesnake
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Raw sequence data and analytical resources for: Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic
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Variation in the resource environment affects patterns of seasonal adaptation at phenotypic and genomic levels in <em>Drosophila melanogaster</em>
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Genomic resources for the little pocket mouse (Perognathus longimembris longimembris)
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Datasets of "Whole genome sequencing of European autochthonous and commercial pig breeds provides selection signatures of adaptation of genetic resources to different breeding and production systems"
<p>Results of the F<sub>ST</sub> and H<sub>P</sub> analyses.</p>
Data from: "De novo transcriptome assembly of the mountain fly Drosophila nigrosparsa using short RNA-seq reads" in Genomic Resources Notes Accepted 1 August 2014-30 September 2014
Drosophila (Drosophila) nigrosparsa is a habitat specialist restricted to the European montane/alpine zone (Bächli 2008). Mountain biodiversity is considered highly vulnerable to ongoing climate warming (IPCC 2013), and organisms at high altitudes have only limited possibility to shift to cooler habitats at elevations above (Pertoldi & Bach 2007). For such species, rapid evolution may offer a solution for long-term survival. We are establishing D. nigrosparsa as a model system to test the extent and tempo of adaptive evolution under thermal stress in the laboratory. In this study, we used Illumina high-throughput sequencing to assemble the species' transcriptome using the pooled mRNA from 22 developmental and physiological stages.
Data from: "Characterization of two Iberian freshwater fish transcriptomes, Squalius carolitertii and Squalius torgalensis, living in distinct environmental conditions" in Genomic Resources Notes Accepted 1 April 2015 to 31 May 2015
The advance of NGS technologies opened exciting research avenues, as for example expanding the study of the mechanisms underlying adaptation from model organisms to natural systems. We used NGS technologies to sequence 12 RNA-seq libraries, and provide the first transcriptomes of two endemic Iberian Cyprinids. The species Squalius carolitertii and S. torgalensis inhabit different regions of Portugal with distinct climate types, Atlantic in the North and Mediterranean in the South, respectively. While northern regions present mild temperatures, in southern regions fish are often under harsh temperatures and droughts. Herein, we sequenced the transcriptome from three tissues (skeletal muscle, liver and fins) in an Illumina HiSeq2000 of fish exposed to different temperatures: 18ºC (control) and 30ºC (test). Around 200 million raw reads were generated for each species, with similar number of reads per library (approximately 30 million), rendering de novo assemblies with a total of 145975 and 137303 contigs, for S. carolitertii and S. torgalensis, respectively. Gene ontology showed that around 60% of the annotated genes belonged to four biological processes and approximately 75% to two molecular functions. Besides, this study provides, for the first time, the transcriptome characterization of two endemic fish from Iberian freshwater basins, S. carolitertii and S. torgalensis, and constitutes a valuable resource for understanding environmental adaptations of Iberian Cyprinids.
Data from: "Polar bear (Ursus maritimus) transcriptome assembly and SNP discovery" in Genomic Resources Notes accepted 1 August 2013-30 September 2013
Polar bears (Ursus maritimus) in the Western Hudson Bay subpopulation have been declining in size and body condition for decades, as climate change causes earlier sea ice breakup, reduced hunting time on the ice, and an increasingly long fasting season. As Western Hudson Bay females have decreased in size, rates of litter production and average litter size have also decreased, while cub mortality and average time to independence have increased. Although these changes have potential evolutionary consequences, little is yet known about the adaptive genetic variation in body size or fat accumulation that would have to underlie any such change. In this study, we used high-throughput Illumina sequencing to develop SNPs from pooled blood and fat transcriptomes, using samples from five adult female polar bears and five (unrelated) dependent cubs. In total, we generated 371,258 transcripts of which 36,755 were deemed to be "full length" (i.e., covered more than 90% of their best BLAST hit), and we identified 63,020 SNPs. Since this study was conducted, we have used a subset of these SNPs to develop an Illumina BeadArray for quantitative genetics research in Western Hudson Bay.
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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.