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ShareScore release 0.9.0
Dataset results
42 results for “targeted sequence capture”
Data from: Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales
Comparative genetic studies of non-model organisms are transforming rapidly due to major advances in sequencing technology. A limiting factor in these studies has been the identification and screening of orthologous loci across an evolutionarily distant set of taxa. Here, we evaluate the efficacy of genomic markers targeting ultraconserved DNA elements (UCEs) for analyses at shallow evolutionary timescales. Using sequence capture and massively parallel sequencing to generate UCE data for five co-distributed Neotropical rainforest bird species, we recovered 776–1516 UCE loci across the five species. Across species, 53–77% of the loci were polymorphic, containing between 2.0 and 3.2 variable sites per polymorphic locus, on average. We performed species tree construction, coalescent modeling, and species delimitation, and we found that the five co-distributed species exhibited discordant phylogeographic histories. We also found that species trees and divergence times estimated from UCEs were similar to the parameters obtained from mtDNA. The species that inhabit the understory had older divergence times across barriers, contained a higher number of cryptic species, and exhibited larger effective population sizes relative to the species inhabiting the canopy. Because orthologous UCEs can be obtained from a wide array of taxa, are polymorphic at shallow evolutionary timescales, and can be generated rapidly at low cost, they are an effective genetic marker for studies investigating evolutionary patterns and processes at shallow timescales.
Data from: Targeted sequence capture and resequencing implies a predominant role of regulatory regions in the divergence of a sympatric lake whitefish species pair (Coregonus clupeaformis)
Latest technological developments in evolutionary biology bring new challenges in documenting the intricate genetic architecture of species in the process of divergence. Sympatric populations of lake whitefish represent one of the key systems to investigate this issue. Despite the value of random genotype-by-sequencing methods and decreasing cost of sequencing technologies, it remains challenging to investigate variation in coding regions, especially in the case of recently duplicated genomes as in salmonids, as this greatly complicates whole genome resequencing. We thus designed a sequence capture array targeting 2773 annotated genes to document the nature and the extent of genomic divergence between sympatric dwarf and normal whitefish. Among the 2728 genes successfully captured, a total of 2182 coding and 10 415 noncoding putative single-nucleotide polymorphisms (SNPs) were identified after applying a first set of basic filters. A genome scan with a quality-refined selection of 2203 SNPs identified 267 outlier SNPs in 210 candidate genes located in genomic regions potentially involved in whitefish divergence and reproductive isolation. We found highly heterogeneous FST estimates among SNP loci. There was an overall low level of coding polymorphism, with a predominance of noncoding mutations among outliers. The heterogeneous patterns of divergence among loci confirm the porous nature of genomes during speciation with gene flow. Considering that few protein-coding mutations were identified as highly divergent, our results, along with previous transcriptomic studies, imply that changes in regulatory regions most likely had a greater role in the process of whitefish population divergence than protein-coding mutations. This study is the first to demonstrate the efficiency of large-scale targeted resequencing for a nonmodel species with such a large and unsequenced genome.
Data from: Sequence Capture using PCR-generated Probes (SCPP): a cost-effective method of targeted high-throughput sequencing for non-model organisms
Recent advances in high-throughput sequencing library preparation and subgenomic enrichment methods have opened new avenues for population genetics and phylogenetics of non-model organisms. To multiplex large numbers of indexed samples while sequencing predominantly orthologous, targeted regions of the genome, we propose modifications to an existing, in-solution capture that utilizes PCR products as target probes to enrich library pools for the genomic subset of interest. The sequence capture using PCR-generated probes (SCPP) protocol requires no specialized equipment, is highly flexible, and significantly reduces experimental costs for projects where a modest scale of genetic data is optimal (25-100 genomic loci). Our alterations enable application of this method across a wider phylogenetic range of taxa and result in higher capture efficiencies and coverage at each locus. Efficient and consistent capture over multiple SCPP experiments and at various phylogenetic distances is demonstrated, extending the utility of this method to both phylogeographic and phylogenomic studies.
Data from: Targeted sequence capture and resequencing implies a predominant role of regulatory regions in the divergence of a sympatric lake whitefish species pair (Coregonus clupeaformis)
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Data from: Comparison of target-capture and restriction-site associated DNA sequencing for phylogenomics: a test in cardinalid tanagers (Aves, genus: Piranga)
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Data from: Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales
Open the record for dataset details and reuse information.
Data from: Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales
Open the record for dataset details and reuse information.
Data from: Sequence Capture using PCR-generated Probes (SCPP): a cost-effective method of targeted high-throughput sequencing for non-model organisms
Open the record for dataset details and reuse information.
Target capture bisulfite sequencing (tcBS-seq) to evaluate clonal methylation inheritance [BiSulfite-seq 2]
GEO Series GSE234029. Mus musculus. 16 samples. Type: Methylation profiling by high throughput sequencing.
Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity with CHANGE-seq-BE [Hybrid Capture Sequencing for CBE and ABE]
GEO Series GSE308237. Homo sapiens. 36 samples. Type: Other.
Targeted single cell RNA-sequencing of transcription factors facilitates biological insights from human cell experimental models [iPSC neuron pre-capture]
GEO Series GSE168590. Homo sapiens. 752 samples. Type: Expression profiling by high throughput sequencing.
Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing
GEO Series GSE146194. Homo sapiens. 11 samples. Type: Expression profiling by high throughput sequencing.
Target capture bisulfite sequencing (tcBS-seq) to evaluate clonal methylation inheritance
GEO Series GSE234695. Mus musculus. 40 samples. Type: Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing.
Targeted single cell RNA-sequencing of transcription factors facilitates biological insights from human cell experimental models [intestinal stromal cells pre-capture]
GEO Series GSE168626. Homo sapiens. 252 samples. Type: Expression profiling by high throughput sequencing.
Classification of cancer cell lines using a promoter-targeted liquid hybridization capture-based bisulfite sequencing approach
GEO Series GSE44866. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing.
A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture
GEO Series GSE61099. Mus musculus; Homo sapiens. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity with CHANGE-seq-BE [Hybrid Capture Sequencing for Cas9]
GEO Series GSE307892. Homo sapiens. 18 samples. Type: Other.
A 3’-end capture sequencing method for high-throughput targeted gene expression profiling
GEO Series GSE190096. Homo sapiens. 720 samples. Type: Expression profiling by high throughput sequencing.
Target capture bisulfite sequencing (tcBS-seq) to evaluate clonal methylation inheritance [BiSulfite-seq]
GEO Series GSE234028. Mus musculus. 8 samples. Type: Methylation profiling by high throughput sequencing.
Target capture bisulfite sequencing (tcBS-seq) to evaluate clonal methylation inheritance [RNA-seq]
GEO Series GSE234024. Mus musculus. 16 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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International Brain Laboratory public data
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OpenNeuro
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