NEB Scientific Posters
Your search returned 78 results.
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A sample-to-results workflow for Respiratory Syncytial Virus (RSV) whole-genome sequencing
RSV, a single-stranded RNA virus, is the leading cause of respiratory illness in infants. Using multiplex targeted amplification sequencing techniques, the presence of RSV in the population can be monitored for mutations that negatively impact treatment efficacy. Here, we describe a newly developed RSV sequencing approach based on amplicon-targeted sequencing for Illumina or Oxford Nanopore Technologies platforms, and featuring the NEBNext RSV Primer Module.
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Matched fresh frozen and FFPE patient tissues reveal the enhanced sensitivity and data quality of a novel DNA library prep method
Formalin-fixed, paraffin-embedded samples are a challenging sample type for most NGS library prep methods. We developed a novel method, compatible with both high and low quality FFPE DNA samples, employing three new enzyme mixes, designed specifically for compatibility with FFPE samples. The NEBNext UltraShear FFPE DNA Library Prep Kit includes an enzymatic fragmentation step that improves the library yield, library metrics, and variant calling accuracy.
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Streamlining RNA and DNA library construction methods to meet the challenges of high-throughput sequencing
With the goal of streamlining the processing of a variety of samples of various input amounts, the NEBNext UltraExpress® library prep kits respond to a user-stated need for faster, more efficient, and easily automated workflows. One key optimization is the single-condition workflow, which enables the simultaneous processing of multiple different sample input amounts (within the kit’s stated input range) with a single adaptor concentration and a single recommendation for PCR cycles. These advances have resulted in a single-tube solution, incorporating master-mixed reagents, reduced incubation times, fewer clean-up steps, and the generation of less plastic waste.
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E5hmC-seq: Detection of 5hmC at single-base resolution
DNA methylation is an epigenetic regulator of gene expression with important functions in development and diseases, such as cancer. Typically, the modified cytosines, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), are detected by sequencing Illumina libraries generated using a gentle, enzyme-based workflow called NEBNext® EM-seq, or by the harsher bisulfite conversion. Here, we describe an enzymatic method that enables specific detection of 5hmC, using the NEBNext Enzymatic 5hmC-seq (E5hmC-seq) Kit.
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Germline variant calling with EM-seq data
NEBNext Enzymatic Methyl-seq (EM-seq) workflows involve base conversion, which can be a challenge for variant detection. In EM-seq, this challenge is overcome using bioinformatic tools. Because methylation information is only preserved on a single strand in EM-seq libraries, the other strand can be used to detect genetic variation. Using this method, we can call germline SNPs with high precision.
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Methods for sequencing cell-free DNA and cell-free RNA from human plasma
cfDNA and cfRNA are nucleic acid fragments found circulating in blood. These nucleic acids originate from various cell types, providing insights into the health of the system as a whole. By evaluating the change in cell-free nucleic acids over time, via serial blood draws, researchers can monitor for atypical biological processes, including cancer. When combined with the new Monarch Mag Viral DNA/RNA Extraction Kit, both the NEBNext Ultra II and the NEBNext UltraExpress library prep kits produce high-quality libraries.
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An end-to-end enzymatic solution for methylomes from low-input DNA
The cytosine modifications 5mC and 5hmC are important regulatory marks within the genome, influencing gene expression. Older techniques of methylome analysis, like bisulfite sequencing, are harsh and can damage the input DNA, decreasing the quality of the resulting libraries. NEBNext Enzymatic Methyl-seq (EM-seq) was introduced in 2019, and brought to bear gentle, enzymatic fragmentation, minimizing damage to the DNA and improving the quality of the resulting libraries. As a further improvement on the EM-seq workflow, NEBNext Enzymatic Methyl-seq v2 has been introduced, requiring lower DNA inputs and offering improved compatibility with lower-quality samples.
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Streamlined whole-genome and targeted sequencing workflows for prevalent RNA viruses: SARS-CoV-2, Respiratory Syncytial Virus, and Influenza A
Monitoring respiratory viruses through whole genome and targeted sequencing is now more important than ever before, particularly in the wake of the global pandemic. We have developed sequencing approaches for respiratory RNA viruses, including SARS-CoV-2, RSV, and Flu, to support scientists and public health laboratories to monitor these critical pathogens.
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Application of High Complexity Golden Gate Assembly to Rapid Engineering of Bacteriophage Genomes
Data-optimized Assembly Design (DAD) enhances Golden Gate Assembly (GGA) by using precise ligation fidelity measurements to select high-accuracy fusion sites. This approach replaces traditional GGA methods, enabling the efficient assembly of multiple parts while minimizing errors. We have developed a set of tools to apply DAD to the design of complex assemblies of up to 36 parts and 50kB final size in a single reaction. Combined with optimized reagents, DAD yields sequence-accurate constructs ready for use without further processing. The small parts are easy to produce via PCR or DNA synthesis and can be manipulated in E. coli plasmid systems, supporting viral mutagenesis and gene swaps. These principles facilitate modular assembly of bacteriophage genomes for high-throughput pathogen research.
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Enhanced Rolling Circle Amplification Performance with a Newly Engineered phi29 DNA Polymerase
Isothermal DNA amplification techniques exponentially increase the amount of DNA in a sample without the constraint of thermocycling. NEB offers a wide range of products for isothermal amplification, including reagents for rolling circle amplification (RCA). The most widely used DNA polymerase for RCA is phi29, which possesses high processivity and fidelity, and strong strand-displacement activity. We recently engineered an improved version of this polymerase, phi29-XT, that shares the same positive characteristics of the wild-type phi29 but also generates a higher yield in less time than the wild-type enzyme. Additionally, while wild-type phi29 works optimally at 30°C, phi29-XT performs best at 42°C. phi29-XT has been used successfully downstream of DNA assembly technologies, such as GoldenGate and NEBuilder HiFi Assembly, to perform high-throughput cell- and vector-free protein expression. Furthermore, the phi29-XT RCA kit also enabled high-throughput fosmid amplification directly from bacterial cells, followed by ONT sequencing for de novo fosmid DNA assembly. Together, these applications demonstrate the utility of the phi29-XT and the RCA kit for isothermal amplification of circular DNA templates.
