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Proximo Hi-C Kit for Plant Samples

1.350,00 

Quantity: 2 rxns

    Please contact us for a quotation

     


    Description

    Proximity Ligation NGS Library Prep from crude plant samples, for Illumina Sequencing.

    The Proximo Hi-C method employs cost-effective proximity ligation data generated using in vivo Hi-C to orient and order contigs into chromosome-scale scaffolds and generate reference-quality plant genome assemblies. Go beyond the sequence to phase haplotypes and detect structural variation; and help deliver on the promise of genomics across a wide range of many applications in agriculture and medicine.

    • Scaffold chromosome-scale plant genomes directly from plant samples
    • No high-molecular-weight DNA extraction required
    • User-friendly complete 2-pack Hi-C kit, including NGS library prep reagents
    • Short-read compatible; yields libraries for Illumina® sequencing
    • Individualized data analysis packages for plant genome scaffolding/assembly, haplotype phasing, variant detection, and interaction analyses are available – please contact us to discuss your project details

    Proximity ligation (Hi-C) libraries are generated from a crude plant sample. Interactions are captured by crosslinking, digesting, and creating chimeric junctions that are sequenced. The Hi-C sequence data may be used in conjunction with shotgun/whole genome sequence data obtained by standard NGS approaches, for genome assembly and scaffolding, haplotype phasing, detection of structural variants, TAD calling, and other interaction analyses.

    Explore the genome organization of any organism

    The genomes of millions of plant species still need to be uncovered. However, newly sequenced plant genomes are typically fragmented, incomplete, interspersed with sequencing and annotation ambiguities and errors, and without critical haplotype information. Phase Genomics´ proximity ligation (Hi-C) technology enables scaffolding optimization to group and order sequencing data into very long contigs and high-quality, chromosome-scale scaffolds. High quality assemblies allow for improved annotation accuracy, thereby facilitating the functional and comparative genomics studies needed to answer important questions in medicine, agriculture and species conservation and evolution. The table below shows how Phase Genomcs´ Hi-C technology also enabled the  genome scaffolding of organisms which were well characterized by conventional sequencing techniques:

     

     

    Proximo Workflow:
    The proximity ligation (Hi-C) library prep reagents provide a streamlined protocol that does not require extraction of high-molecular weight (HMW) DNA. The processing guidelines for different types of animal samples ensure robust results. The 8-step library prep workflow can be completed in 2 working days, and requires only 3 hours of hands-on time. The protocol contains several convenient, safe stopping points. Sequencing may be performed on any Illumina® sequencer. The Proximo Kit yields a dual-indexed proximity ligation library, for which ~50 to 100 million paired-end reads are required. For analyzing your Hi-C sequence data, you also need draft assembly sequencing data of your samples, which may be performed with a suitable library preparation kit of your choice – contact us for recommendations or to discuss a service project if you do not have prior experience with shotgun/whole genome library preparation and sequencing.

     

    Data analysis is offered optionally as a customized service, e.g. Phase Genomics´ Proximo Genome Scaffolding platform utilizing a three-stage genome scaffolding algorithm. Hi-C Proximo data may also be integrated with other computational approaches (e.g. FALCON-Phase), to enable the production of “gold” and “platinum” plant genomes.
    The open source software FALCON-Phase combines Proximo data with the high accuracy, long-read sequencing data from PacBio®, enabling researchers to create haplotype-resolved genome sequences on a chromosomal scale.

    Please contact us to let us know your project details and receive a quote..

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