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10 results for “bait design”
Whole-genome capture and sequencing of Mycobacterium tuberculosis directly from clinical samples - Design of RNA oligonucleotide baits for Agilent Technologies' SureSelect target enrichment
<p>This dataset comprises the sequence of <strong>44 278 RNA oligonucleotide "baits" (120 bp each) </strong>designed to perform <strong>whole-genome capture and sequencing of <em>Mycobacterium tuberculosis</em> directly from clinical samples</strong> (DNA) using Agilent Technologies’ SureSelect target enrichment system following the Illumina paired-end multiplexed sequencing library protocol. </p> <p>RNA oligonucleotide “baits” were designed to span the ∼4.5 Mb of the <em>M. tuberculosis</em> genome. In brief, the reference genome sequence of the MTBC H37Rv strain (Genbank #AL123456) was <em>in silico</em> fragmented into 120 bp sequences twice, to ensure an overlap of 60 bp between sequences. Due to their rich GC content, which could interfere with DNA capture, all MTBC genes of the PE, PPE and PE-PGRS family were also independently fragmented into 120 bp sequences, in order to increase capture sensitivity. All resulting sequences were BLASTn searched against the Human Genomic + Transcript database to excluded homologous sequences to the human genome. Overall, a total of 42,278 RNA probes were generated and this custom bait library was then uploaded to the SureDesign software (https://earray.chem.agilent.com/suredesign) and synthesized by Agilent Technologies. During synthesis, the 2198 sequences complementary to the PE, PPE and PE-PGRS family were unbalanced 8:1 to potentiate capture.</p> <p>More details can be found in the following publication:</p> <p>- Macedo, R., Isidro, J., Ferreira, R., Pinto, M., Borges, V., Duarte, S., Vieira, L., & Gomes, J. P. (2023). Molecular Capture of <em>Mycobacterium tuberculosis</em> Genomes Directly from Clinical Samples: A Potential Backup Approach for Epidemiological and Drug Susceptibility Inferences. <em>International journal of molecular sciences</em>, <em>24</em>(3), 2912. https://doi.org/10.3390/ijms24032912</p>
Set of 4 597 baits designed in collaboration with RapidGenomics (Gainesville, Florida, USA) to capture the identified low‐ to single‐copy nuclear genes (LSCN).
<p>This dataset presents a set of 4,597 baits designed in collaboration with RapidGenomics (Gainesville, Florida, USA) to capture the identified low- to single-copy nuclear genes (LSCN) in our study. These baits were instrumental in our research on the evolutionary relationships of the Neotropical magnolias based on plastome and nuclear phylogenomics. The data provided are crucial for understanding the methodology and results of our study.</p>
'Baiting' room design for Beasts of London 2019
3D Visualisation of Scenic Design for 'Baiting' room at Museum of London's Beasts exhbition. Video content projection mapped on internal surfaces of wooded baiting pen surrounded by painted cut out figures Scale = 1:1 Back wall removed for viewing purposes Source: Objaverse 1.0 / Sketchfab
Figs. 14–15. Trap design. 14 in The Dung- and Carrion-Feeding Scarabs (Coleoptera: Scarabaeoidea) of an Amazonian Blackwater Rainforest: Results of a Continuous, 56-Week, Baited-PitfallTrap Study
Figs. 14–15. Trap design. 14) Completed trap with rain cover in position; 15) Close-up showing attachment of bait vial inside lip of collecting bottle.
Figs. 11–13. Trap design. 11 in The Dung- and Carrion-Feeding Scarabs (Coleoptera: Scarabaeoidea) of an Amazonian Blackwater Rainforest: Results of a Continuous, 56-Week, Baited-PitfallTrap Study
Figs. 11–13. Trap design. 11) Pitfall trap components: PVC pipe in the ground, collecting bottle with bait vial attached just inside of opening, soil cover, rain cover; 12) Collecting bottle placed inside of PVC pipe so that the lip of the bottle is flush with the surface of the ground; 13) Soil cover placed over lip of collecting bottle.
Figure 1. Baited trap made with 500 in Is the capture success of orchid bees %Hymenoptera, Apoidea) influenced by different baited trap designs? A case study from southern Brazil
Figure 1. Baited trap made with 500 mL bottle; left landing platform not shown to indicate position of the entrance hole.
Data from: Insight from an ultraconserved element bait set designed for hemipteran phylogenetics integrated with genomic resources
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Data from: Identifying conserved genomic elements and designing universal bait sets to enrich them
Targeted enrichment of conserved genomic regions is a popular method for collecting large amounts of sequence data from non-model taxa for phylogenetic, phylogeographic and population genetic studies. For example, two available bait sets each allow enrichment of thousands of orthologous loci from >20 000 species (Faircloth et al. Systematic Biology, 61, 717–726, 2012; Molecular Ecology Resources, 15, 489–501, 2015). Unfortunately, few open-source workflows are available to identify conserved genomic elements shared among divergent taxa and to design enrichment baits targeting these regions. Those that do exist require extensive bioinformatics expertise and significant amounts of time to use. These shortcomings limit the application of targeted enrichment methods to additional organismal groups. Here, I describe a universal workflow for identifying conserved genomic regions in available genomic data and for designing targeted enrichment baits to collect data from these conserved regions. These methods require less expertise, less time and better use commonly available information to identify conserved loci and design baits to capture them. I apply this computational approach to the understudied arthropod groups Arachnida, Coleoptera, Diptera, Hemiptera or Lepidoptera to identify thousands of conserved loci in each group and design target enrichment baits to capture these loci. I then use in silico analyses to demonstrate that targeted enrichment of the conserved loci can be used to reconstruct the accepted relationships among genome sequences from the focal arthropod orders. The software workflow I created allowed me to identify thousands of conserved loci in five diverse arthropod groups and design sequence capture baits to target them. This suite of capture bait designs should enable collection of phylogenomic data from >900 000 arthropod species. Although the examples in this manuscript focus on understudied arthropod groups, the approach I describe is applicable to all organismal groups having some form of pre-existing genomic information (e.g. other invertebrates, plants, fungi and microbes). Finally, the documentation, design steps, software code and bait sets developed here are available under an open-source license for restriction-free testing, use, and additional modification by any research group.
Data from: Identifying conserved genomic elements and designing universal bait sets to enrich them
Open the record for dataset details and reuse information.
CLIP-Seq Analysis Enables the Design of Ribosomal RNA Bait Oligonucleotides That Protect Against C9ORF72 ALS/FTD-Associated Poly-GR Pathophysiology
GEO Series GSE182008. Homo sapiens. 5 samples. Type: Other.
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