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Dataset results
660 results for “Genome assemblies”
Chromosome-scale assembly of hexaploid genome of Ma Bamboo (Dendrocalamus latiflorus Munro)
GEO Series GSE155494. Dendrocalamus latiflorus. 24 samples. Type: Expression profiling by high throughput sequencing.
Genome assemblies related to preprint "European Farmhouse Brewing Yeasts Form a Distinct Genetic Group"
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De Novo Assembly of Plasmodium knowlesi Genomes From Clinical Samples Explains the Counterintuitive Intrachromosomal Organization of Variant SICAvar and kir Multiple Gene Family Members
<p>Published DOI: <a href="https://doi.org/10.3389/fgene.2022.855052">https://doi.org/10.3389/fgene.2022.855052</a></p> <p>Supporting data for the attached publication. De Novo assembled genomes of <em>Plasmodium knowlesi</em> generated using Nanopore long reads. Supporting statistical results are included. Variant call files from structural variant calls are attached for each genome. Additionally, statistical results from BUSCO, QUAST, Pomoxis and AGAT are included. Annotation files in GFF3 format including further analyses of these annotation files are attached. Scripts for post analysis are attached with scripts for data generation presented on Github repository: "Pknowlesi_denovo_genome_assembly"</p>
Galleria mellonella genome assembly (wild wax worm)
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Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling [ChIP-seq]
GEO Series GSE120750. Drosophila virilis; Drosophila busckii. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Whole genome sequencing and assembly of Eukaryotic microbes isolated from ISS environmental surface, Kirovograd region soil, Chernobyl Nuclear Power Plant and Chernobyl Exclusion Zone
The whole-genome sequences of eight fungal strains that were selected for exposure to microgravity at the International Space Station are presented here. These baseline sequences will help to understand the observed production of novel bioactive compounds.
Whole genome sequencing and assembly of Eukaryotic microbes isolated from ISS environmental surface Kirovograd region soil Chernobyl Nuclear Power Plant and Chernobyl Exclusion Zone
The whole-genome sequences of eight fungal strains that were selected for exposure to microgravity at the International Space Station are presented here. These baseline sequences will help to understand the observed production of novel bioactive compounds.
Lower eukaryotic isolates belonging to class Tremellomycetes isolated from International Space Station Genome sequencing and assembly
Genome sequencing and assembly of lower Eukaryotic isolates belonging to class Tremellomycetes isolated from International Space Station
Genome assembly of 12 Nigrospora species Assembly
GEO Series GSE270150. Nigrospora rubi. 12 samples. Type: Expression profiling by high throughput sequencing.
Comparative multi-omic analyses of Trichinella Pseudospiralis based on a new genome assembly by long-read sequencing
GEO Series GSE113105. Trichinella pseudospiralis. 6 samples. Type: Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing.
Genome assembly of silkworm BmN4 cells
GEO Series GSE288600. Bombyx mori. 12 samples. Type: Non-coding RNA profiling by high throughput sequencing.
De novo assembly and annotation of the singing mouse genome
GEO Series GSE212957. Scotinomys teguina. 17 samples. Type: Expression profiling by high throughput sequencing; Other.
Genome assemblies of the sugarcane orange rust fungal pathogen Puccinia kuehnii
<p><em>Puccinia kuehnii</em>is an obligate biotrophic fungal pathogen that causes orange rust of sugarcane, which is prevalent in many countries around the globe. In the USA, orange rust was first detected in sugarcane in Florida in 2007 and poses a persistent and economically damaging threat to the sugarcane industry in this region. Here, we generated the first genome assemblies for two isolates of <em>P. kuehnii </em>(1040 and 2143) collected in Florida in 2017 from two sugarcane cultivars, CL85-1040 and CP89-2143, respectively. These two rust genome resources will be of immense value for future genomic studies, particularly further exploration of the predicted secretomes that may help define key pathogenicity determinants for this economically important pathogen.</p>
De novo assembled individual genome does not show advantage against standard reference genome: a demonstration of Chinese Han Population
GEO Series GSE121013. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
GEO Series GSE165787. Zea mays. 104 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Gene annotations for <i>Strix occidentalis caurina</i> draft nuclear genome assembly version 1
<p><strong>NSO-wgs-v1-nuc.gff.bz</strong> : This file provides the gene annotations produced by the MAKER pipeline for the <em>Strix occidentalis caurina</em> draft whole nuclear genome assembly, NSO-wgs-v1-nuc.</p> <p><strong>NSO-wgs-v1-nuc-masked-homology-includes-LowComplexity.out.bz</strong> : This file provides the repeat annotations produced by the homology-based masking of NSO-wgs-v1-nuc that included masking of low complexity regions and simple repeats.</p> <p><strong>NSO-wgs-v1-nuc-masked-DeNovo-includes-LowComplexity.out</strong> : This file provides the repeat annotations produced by the <em>de novo</em> masking of NSO-wgs-v1-nuc that included masking of low complexity regions and simple repeats.</p> <p><strong>NSO-wgs-v1-nuc-masked-homology-no-LowComplexity.out.bz</strong> : This file provides the repeat annotations produced by the homology-based masking of NSO-wgs-v1-nuc that did not include masking of low complexity regions and simple repeats.</p> <p><strong>NSO-wgs-v1-nuc-masked-DeNovo-no-LowComplexity.out</strong> : This file provides the repeat annotations produced by the <em>de novo</em> masking of NSO-wgs-v1-nuc that did not include masking of low complexity regions and simple repeats.</p>
High quality de novo long read genome assembly and annotation of resistance protein families for saw toothed grain beetle-Supplementary
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The haplotype-resolved genome assemblies of the hybrid Pinot Noir
<p>The haplotype-resolved genome assemblies of the hybrid Pinot Noir, PN1(495.185MB) and PN2(489.609 MB).<br> To validate the quality of our assembly, K-mer and BUSO0 were conducted. We used K-mer to evaluate genomic heterozygosity, estimated 1.43%. BUSCO to evaluate genomic completeness about 98.3% in PN1 of thecore conserved plant genes were found complete in the genome assembly. For genome annotation, the number of genesidentified by the genome is similar, more than 33,803 genes were found for Pinot Noir, PN1<br> The PN1 genome assembly: PNhap1.v1. fa<br> The PN1gene annotation: PNhap1.v1. gff3<br> The PN1 TE annotation: PNhap1_TE.v1.gff<br> The PN2 genome assembly: PNhap2.v1. fa</p>
Multiple Origins of Chalcone Synthase Short Interfering RNAs in Glycine max Revealed by Genome Assemblies of Mutant Alleles
GEO Series GSE239923. Glycine max. 46 samples. Type: Expression profiling by high throughput sequencing.
Genome assembly, with and without masking
<p>Genome assembly, with and without masking</p>
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.