Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
98
datasets available to search
ShareScore release 0.9.0
Dataset results
98 results for “pooled sequencing”
Variant Data from Pooled Sequencing of Hybrid Kiwifruit
<p>Variant data from pooled sequencing of hybrid <em>Actinidia</em> families segregating for fruit size and Vitamin C Content.</p>
Pooled DNA sequencing to identify SNPs associated with a major QTL for bacterial wilt resistance in Italian ryegrass (Lolium multiflorum Lam.)
<p>We used pooled DNA sequencing to characterize a major QTL for bacterial wilt resistance of Italian ryegrass and to develop inexpensive sequence-based markers to efficiently target resistance alleles for marker-assisted recurrent selection. From the mapping population segregating for the QTL, DNA of 44 of the most resistant and 44 of the most susceptible F<sub>1</sub> individuals were pooled and sequenced using the Illumina HiSeq2000 platform. Allele frequencies of 18 x 10<sup>6</sup> single nucleotide polymorphisms (SNP) were determined in the resistant and susceptible pool. A total of 271 SNPs on 140 scaffold sequences of the reference parental genome showed significantly different allele frequencies in both pools. We converted 44 selected SNPs to KASP markers, genetically mapped these proximal to the major QTL and thus validated their association with bacterial wilt resistance.</p>
Data from: Using transcriptome sequencing and pooled exome capture to study local adaptation in the giga-genome of Pinus cembra
Open the record for dataset details and reuse information.
Resolution, validation and divergence of heterozygous haplotypes from pooled long read sequencing of the diamondback moth (Lepidoptera: Plutellidae)
<p>This data sets includes the full set of intermediate genome assemblies produced during our analyses. We make these available for researchers who may be interested in the variation between assembly results and variation within the study organism (<em>Plutella xylostella</em>) prior to removal during subsequent genome processing.</p>
Data and processing scripts for PRISM barcode sequencing data used in "Massively parallel pooled screening reveals genomic determinants of nanoparticle-cell interactions"
<p>Sequencing data for the PRISM barcodes generated after nano-particle treatment is presented in this repository alongside the code to process the sequencing counts to generate the binning probabilities and weighted scores. <br> <br> For the details please see the original publication or the bioarxiv preprint: https://doi.org/10.1101/2021.04.05.438521<br> <br> The raw data is provided in PILOT_DATA_COUNTS.csv and EXPERIMENT_DATA_COUNTS.csv files, for the pilot and the actual experiment. <br> <br> For each of these files an R script is provided to process them, along with the output of the scripts (PILOT_DATA_PROBABILITIES.csv and EXPERIMENT_DATA_PROBABILITIES.csv)</p>
Structural variants in the barley gene pool: precision and sensitivity to detect them using short-read sequencing and their association with gene expression and phenotypic variation
<p>SNV of 23 parental barley inbreds of the double round robin population (DRR) (<a href="https://doi.org/10.1111/pbi.13746">https://doi.org/10.1111/pbi.13746</a>) used in the publication "Structural variants in the barley gene pool: precision and sensitivity to detect them using short-read sequencing and their association with gene expression and phenotypic variation". SV, INDELs, and additional data are available via figshare (https://doi.org/10.6084/m9.figshare.16802473).</p>
Improving the efficiency of single cell genome sequencing based on overlapping pooling strategy
Single cell genome sequencing has become a useful tool in medicine and biology studies. However, an independent library is required for each cell in single cell genome sequencing, so that the cost grows in step with the number of cells. In this study, we report a study on efficient single-cell copy number variation (CNV) analysis based on overlapping pooling strategy together with branch and bound (B&B) algorithm. Single cells are overlapped pooled before sequencing, and later are assorted into specific types by estimating their CNV patterns by B&B algorithm. Instead of constructing libraries for each cell, a library is required only for each pool. As long as the number of pools is smaller than the cells, fewer libraries are needed, and a lower cost is spent. Through computer simulations, we overlapping pooled 80 cells into 40 and 27 pools and classified them into cell types based on CNV pattern. The results showed that 84% cells in 40 pools and 76.5% cells in 27 pools were correctly classified on average, while only half or one-third of the sequencing libraries are required. Combining with traditional approaches, our method is expected to significantly improve the efficiency of single cell genome sequencing.
Improving the efficiency of single cell genome sequencing based on overlapping pooling strategy
Open the record for dataset details and reuse information.
Data from: Parallel tagged next-generation sequencing on pooled samples – a new approach for population genetics in ecology and conservation
Next-generation sequencing (NGS) on pooled samples has already been broadly applied in human medical diagnostics and plant and animal breeding. However, thus far it has been only sparingly employed in ecology and conservation, where it may serve as a useful diagnostic tool for rapid assessment of species genetic diversity and structure at the population level. Here we undertake a comprehensive evaluation of the accuracy, practicality and limitations of parallel tagged amplicon NGS on pooled population samples for estimating species population diversity and structure. We obtained 16S and Cyt b data from 20 populations of Leiopelma hochstetteri, a frog species of conservation concern in New Zealand, using two approaches – parallel tagged NGS on pooled population samples and individual Sanger sequenced samples. Data from each approach were then used to estimate two standard population genetic parameters, nucleotide diversity (π) and population differentiation (FST), that enable population genetic inference in a species conservation context. We found a positive correlation between our two approaches for population genetic estimates, showing that the pooled population NGS approach is a reliable, rapid and appropriate method for population genetic inference in an ecological and conservation context. Our experimental design also allowed us to identify both the strengths and weaknesses of the pooled population NGS approach and outline some guidelines and suggestions that might be considered when planning future projects.
Data from: Utility of pooled sequencing for association mapping in non-model organisms
High density genome-wide sequencing increases the likelihood of discovering genes of major effect and genomic structural variation in organisms. While there is an increasing availability of reference genomes across broad taxa, the greatest limitation to whole-genome sequencing of multiple individuals continues to be the costs associated with sequencing. To alleviate excessive costs, pooling multiple individuals with similar phenotypes and sequencing the homogenized DNA (Pool-Seq) can achieve high genome coverage, but at the loss of individual genotypes. Although Pool-Seq has been an effective method for association mapping in model organisms, it has not been frequently utilized in natural populations. To extend bioinformatic tools for rapid implementation of Pool-Seq data in non-model organisms, we developed a pipeline called PoolParty and illustrate its effectiveness in genetic association mapping. Alignment expectations based on five pooled Chinook salmon (Oncorhynchus tshawytscha) libraries showed that approximately 48% genome coverage per library could be achieved with reasonable sequencing effort. We additionally examined male and female O. tshawytscha libraries to illustrate how Pool-Seq techniques can successfully map known genes associated with functional differences among sexes such as growth hormone 2. Finally, we compared pools of individuals of different spawning ages for each sex to discover novel genes involved with age at maturity in O. tshawytscha such as opsin4 and transmembrane protein19. While not appropriate for every system, Pool-Seq data processed by the PoolParty pipeline is a practical method for identifying genes of major effect in non-model organisms when high genome coverage is necessary and cost is a limiting factor.
Neutral and adaptive drivers of genomic change in introduced brook trout (Salvelinus fontinalis) populations revealed by pooled sequencing
<p>Understanding the drivers of successful species invasions is important for conserving native biodiversity and for mitigating the economic impacts of introduced species. However, whole-genome resolution investigations of the underlying contributions of neutral and adaptive genetic variation in successful introductions are rare. Increased propagule pressure should result in greater neutral genetic variation, while environmental differences should elicit selective pressures on introduced populations, leading to adaptive differentiation. We investigated neutral and adaptive variation among nine introduced brook trout (<em>Salvelinus fontinalis</em>) populations using whole-genome pooled sequencing. The populations inhabit isolated alpine lakes in western Canada and descend from a common source, with an average of ~19 (range of 7-41) generations since introduction. We found some evidence of bottlenecks without recovery, no strong evidence of purifying selection, and little support that varying propagule pressure or differences in local environments shaped observed neutral genetic variation differences. Putative adaptive loci analysis revealed non-convergent patterns of adaptive differentiation among lakes with minimal putatively adaptive loci (0.001%-0.15%) that did not correspond with tested environmental variables. Our results suggest that (i) introduction success is not always strongly influenced by genetic load, (ii) observed differentiation among introduced populations can be idiosyncratic, population-specific, or stochastic, and (iii) conservatively, in some introduced species, colonization barriers may be overcome by support through one aspect of propagule pressure or benign environmental conditions.</p>
An evaluation of pool-sequencing transcriptome-based exon capture for population genomics of non-model species.
<p>This archive is associated with the article “An evaluation of pool-sequencing transcriptome-based exon capture for population genomics of non-model species.”. Authors: Emeline Deleury, Thomas Guillemaud, Aurelie Blin & Eric Lombaert.</p> <p>The archive contains :<br> - The sequences of the 5,717 Harmonia axyridis randomly selected CDS (5717-targeted-CDS-sequences.gff3, sequence in FASTA format at the end of the file)<br> - For the subset of 3,161 targeted CDS that have a genomic match over their entire length, the positions of exons on transcripts (3161-targeted-CDS-EXON-POSITIONS.csv)</p>
Repeatome turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets
<p>The present repository provides zipped archives containing the results of the RepeatExplorer2 runs of individual as well as comparative repeat analyses in beet genomes.</p> <p> </p> <p>Sugar beet (<em>Beta vulgaris</em> subsp. <em>vulgaris</em>) and its crop wild relatives share a base chromosome number of nine and similar chromosome morphologies. Yet, interspecific breeding is impeded by chromosome and sequence divergence that is still not fully understood. Since repetitive DNA sequences represent the fastest evolving parts of the genome, they likely impact genomic variability and contribute to the separation of beet gene pools. Hence, we investigated if innovations and losses in the repeatome can be linked to chromosomal differentiation and speciation.</p> <p>We traced genome- and chromosome-wide evolution across sugar beet and twelve wild beets comprising all sections of the beet genera <em>Beta </em>and <em>Patellifolia</em>. For this, we combined data from short and long read sequencing, flow cytometry, and cytogenetics to build a comprehensive data framework for our beet panel that spans the complete scale from DNA sequence to chromosome up to the genome. Genome sizes and repeat profiles reflect the separation of the beet species into three gene pools. These gene pools harbor repeats with contrasting evolutionary patterns: We identified section- and species-specific repeat emergences and losses, e.g. of the retrotransposons causal for genome expansions in the section <em>Corollinae</em>/<em>Nanae</em>. Since most genomic variability was found in the satellite DNAs, we focused on tracing the 19 beetSat families across the three beet sections/genera. These taxa harbor evidence for contrasting strategies in repeat evolution, leading to contrasting satellite DNA profiles and fundamentally different centromere architectures, ranging from chromosomal uniformity in <em>Beta</em> and <em>Patellifolia</em> species to the formation of patchwork chromosomes in <em>Corollinae/Nanae</em> species. </p> <p>We show that repetitive DNA sequences are causal for genome size expansion and contraction across the beet genera, providing insights into the genomic underpinnings of beet speciation. Satellite DNAs in particular vary considerably among beet taxa, leading to the evolution of distinct chromosomal setups. These differences likely contribute to the barriers in beet breeding between the three gene pools. Thus, with their isokaryotypic chromosome sets, beet genomes present an ideal system for studying the link between repeats, genome variability, and chromosomal differentiation/evolution and provide a theoretical basis for understanding barriers in crop breeding.</p>
Data from: Utility of pooled sequencing for association mapping in non-model organisms
Open the record for dataset details and reuse information.
Data from: Capturing the population structure of microparasites: using ITS-sequence data and a pooled DNA approach
Open the record for dataset details and reuse information.
Data from: Next-generation sequencing for molecular ecology: a caveat regarding pooled samples
Open the record for dataset details and reuse information.
Data from: How to optimize the precision of allele and haplotype frequency estimates using pooled-sequencing data
Open the record for dataset details and reuse information.
Data from: Parallel tagged next-generation sequencing on pooled samples – a new approach for population genetics in ecology and conservation
Open the record for dataset details and reuse information.
Neutral and adaptive drivers of genomic change in introduced brook trout (Salvelinus fontinalis) populations revealed by pooled sequencing
Open the record for dataset details and reuse information.
Pooled whole genome sequencing from year 2004 and Early-Late SNP data from year 2014
<p>Speciation underlies the generation of novel biodiversity. Yet, there is much to learn about how natural selection shapes genomes during speciation. Selection is assumed to act against gene flow at barrier loci, promoting reproductive isolation. However, evidence for gene flow and selection is often indirect and we know very little about the temporal stability of barrier loci. Here we utilize haplodiploidy to identify candidate male barrier loci in hybrids between two wood ant species. As ant males are haploid they are expected to reveal recessive barrier loci, which can be masked in diploid females if heterozygous. We then test for barrier stability in a sample collected ten years later and use survival analysis to provide a direct measure of natural selection acting on candidate male barrier loci. We find multiple candidate male barrier loci scattered throughout the genome. Surprisingly, a proportion of them are not stable after ten years, natural selection apparently switching from acting against to favoring introgression in the later sample. Instability of barrier effect and natural selection for introgressed alleles could be due to environment-dependent selection, emphasizing the need to consider temporal variation in the strength of natural selection and the stability of barrier effect at putative barrier loci in future speciation work.</p>
ScienceDex guides
Understand access before you commit
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.