Optimized Cell Free Library Prep for Ion Torrent-Based Platforms

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Bioo Scientific has just launched the NEXTflex™ Cell Free DNA Sequencing Kit for Ion PGM™ and Ion Proton™ today. It is designed to prepare genomic DNA-Seq NGS libraries from 1 – 5 ng of cell free DNA for sequencing using Life Technologies’ Ion Torrent PGM and Ion Proton sequencing platforms.

Cell-free DNA is detectable in circulating blood. It has the potential to be used to identify tumor markers for the diagnosis and prognosis, as well as the early detection, of cancer. Additionally, cell free fetal DNA can be isolated from circulating blood allowing for early, non-invasive fetal screening.

With low input requirements, an easily automatable protocol and the ability to multiplex up to 64 samples, the NEXTflex Cell Free DNA Sequencing Kit for Ion PGM and Ion Proton has been optimized to simplify cell free DNA-Seq analysis.

Read more about how the NEXTflex Cell Free DNA Sequencing Kit for Ion PGM™ and Ion Proton can improve your cfDNA and ctDNA analysis.

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Integrative Analysis of 111 Reference Human Epigenomes

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Today Nature published an Integrative analysis of 111 reference human epigenomes in an open access article aimed at creating a reference collection of human epigenomes for primary cells and tissues as a resource analogous to the reference human genome. This is the largest collection so far, produced by the NIH Roadmap Epigenomics Consortium.

The NIH Roadmap Epigenomics Program was established with the goal of elucidating how epigenetic processes contribute to human biology and disease. To this end, the researchers have developed profiles for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. They have established global maps of regulatory elements and defined regulatory modules of coordinated activity and their likely activators and repressors. Disease- and trait-associated gene variants were found to be enriched in tissue-specific epigenomic marks, revealing relevant cell types for human traits, and providing a new resource for interpreting the molecular basis of human disease. Epigenetic differences underlie many challenges to precision medicine, such as variable penetrance and expressivity of genotypes known to contribute to “genetic” diseases, by influencing expression of encoded proteins and regulatory RNAs.

Methods used to develop these reference epigenomes include MethylC-seq, a 2-d protocol that enables the genome-wide identification of cytosine DNA methylation states at single-base resolution. Mark A Urich, Joseph R Nery, Ryan Lister, Robert J Schmitz and Joseph R Ecker of Howard Hughes Medical Institute and The Salk Institute, researchers of the NIH Roadmap Epigenomics Consortium, describe their MethylC-seq protocol in Nature Protocols. This specially designed protocol allows for the identification of DNA methylation features which are not readily apparent from traditional bisulfite-PCR methods, such as the identification of non-CG methylation in human embryonic stem cells and brain tissues, and the identification of large partially methylated domains in animal genomes. Their method was developed using the NEXTflex Bisulfite-Seq Barcodes, eliminating the need for targeted primer design and thereby eliminating the associated biases.

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Using the NEXTflex Rapid DNA-Seq Kit with Custom Baits from MYcroarray for Target Capture

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Dr. Gustafsson from the Department of Biological and Environmental Sciences at the University of Gothenburg recently released an article, Sequence Capture (hybrid enrichment) – an overview, describing how the NEXTflex Rapid DNA-Seq Kit can be used in conjunction with the custom baits from MYcroarray for target capture and subsequent Illumina sequencing.

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Bioo Scientific Partners with the Icahn School of Medicine at Mount Sinai to Reduce Ligation Bias in Next Generation Sequencing

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Bioo Scientific’s latest press release, Bioo Scientific Partners with the Icahn School of Medicine at Mount Sinai to Reduce Ligation Bias in Next Generation Sequencing, announces our partnership with the Icahn School of Medicine at Mount Sinai to bring to market randomized adapter technology to reduce ligation bias in NGS. This partnership makes bias-reducing randomized adapter technology available to all researchers, allowing them to improve the accuracy of their small RNA-Seq analysis.

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Improved Library Prep Offers Higher Percentage of On-target Reads and Better Coverage for SureSelectXT2 Target Capture

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The NEXTflex™ Pre- and Post- Capture Combo Kit (Agilent SureSelectXT2 Compatible) offers all reagents required upstream and downstream of probe hybridization to prepare sequence-ready, multiplexed capture libraries compatible with all SureSelectXT2 bait sets. Read the whitepaper, Improved Library Prep Offers Higher Percentage of On-target Reads and Better Coverage for SureSelectXT2 Target Capture, to learn how the NEXTflex barcode blocker technology improves binding efficiency through index-specific blocking oligos, greatly reducing the number of off-target reads encountered in small and large target capture assays. Furthermore, utilization of NEXTflex reagents with the SureSelectXT2 bait set improves target capture efficiency through robust library preparation workflow, as well as offering important hybridization efficiency improvements.

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Improved Library Prep for SureSelect Target Capture

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Bioo Scientific has added another kit to its line of kits designed to reduce bias and increase the sensitivity, flexibility and speed of NGS library preparation. The new NEXTflex™ Pre- and Post- Capture Combo Kit (Agilent SureSelectXT2 Compatible) is a complete Illumina-compatible library prep solution containing all reagents required upstream and downstream of probe hybridization to prepare sequence-ready, multiplexed capture libraries compatible with all Agilent’s SureSelectxt2 target capture systems. The NEXTflex Pre- and Post- Capture Combo Kit (Agilent SureSelectXT2 Compatible) offers a faster library prep protocol producing libraries with a higher percentage of on-target reads, more robust amplification, and better coverage than competitors’ kits. This kit can be used to improve the performance of any of Agilent’s SureSelectXT2 custom and pre-defined panels.

Read more to learn how to speed up and improve your SureSelectXT2 target capture experiments.

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Reducing Small RNA Sequencing Biases

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A new tutorial posted on GEN, Reducing Small RNA Sequencing Biases, describes how using a randomized adapter strategy during library preparation reduces ligation bias, increasing the accuracy of small RNA-Seq. This bias-reducing randomized adapter technology has been incorporated into Bioo Scientific’s NEXTflex Small RNA-Seq Kit v2, allowing researchers studying small RNAs to make discoveries that may otherwise have been overlooked, and allowing for a greater understanding of many aspects of small RNA biology.

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Constructing High Quality RNA-Seq Libraries from Limited Amounts of Total RNA

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RNA-Seq is a powerful tool that allows researchers to discover, profile and quantify RNA transcripts across the entire transcriptome. One of the primary challenges for RNA-Seq applications is obtaining high-quality data from low input amounts of starting material, as messenger RNA only makes up approximately 0.5%-3% of total RNA. Additionally, the large number of processing steps required to generate RNA-Seq libraries presents additional challenges for efficiency and retention of material throughout each step. The study presented in the whitepaper, Constructing High Quality RNA-Seq Libraries from Limited Amounts of Total RNA, demonstrates that high-quality libraries are readily produced from as little as 10 ng of total RNA using the NEXTflex™ Rapid Directional RNA-Seq Kit.

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Improving on cfDNA isolation kit with mag-bead based NextPrep-Mag™ cfDNA Isolation Kit

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Bioo Scientific’s new NextPrep-Mag™ cfDNA Isolation Kit is designed for extracting cell-free DNA (cfDNA) from 0.6 mL of human blood plasma using a magnetic bead format. The DNA isolated using this kit is ideal for next generation sequencing and PCR analysis.

Many commercial kits for extraction of cell-free DNA from blood are based on solid-phase extraction of DNA on silica filters. Limitations of this method include low sample volumes, a tendency for clogging, and carryover of ethanol used in wash solutions. Silica filter DNA isolation methods also pose difficulties for automation.

Read about how the NextPrep-Mag cfDNA Isolation Kit overcomes these limitations of silica filters DNA isolation kits using a magnetic bead approach, on our data page here.

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Improved Rapid Stranded RNA-Seq

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Bioo Scientific’s new whitepaper, Improved Rapid Stranded RNA-Seq, examines rRNA removal, library yield, and overall quality metrics, demonstrating the effectiveness of the NEXTflex Poly(A) Beads and the NEXTflex Rapid Directional RNA-Seq Kit for providing high quality library preparation solutions for next generation sequencing. To assess the overall quality of our kit, we compared libraries prepared using NEXTflex™ Poly(A) Beads and NEXTflex Rapid Directional RNA-Seq Kit to those prepared with a competitor’s equivalent products.

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