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1.  BA Fast Highly Multiplexed Solution to NGS Library Prep with Low Nanogram DNA Input 
As the quantity of data generated per next generation sequencing (NGS) run increases and the time required per run decreases, the ability to quickly produce and track large numbers of libraries is becoming increasingly important. In addition, the ability to produce high quality libraries from limited starting material and multiple sample types, including FFPE is essential. To overcome these challenges and to minimize the bottleneck of NGS library prep, we have developed a fast, streamlined DNA library preparation method using novel reagents and adaptors. This method accommodates a wide range of sample input quantities and types including genomic, ChIP and fragmented DNA (e.g. FFPE). Data analysis of libraries constructed from as little as 250 pg of ChIP DNA show high complexity and significant overlap of target peaks with libraries made from10 ng of DNA. We have extended the utility of this library prep method by developing additional adaptor and primer reagents. These include a dual barcoding approach that is compatible with Illumina library prep and our novel NEBNext adaptor. This approach enables multiplexing of up to 96 different samples, which can be used to increase the number of samples per flow cell, and/or to identify specific samples/libraries in a lab. Together, the simple, streamlined workflow and dual barcode approach, significantly reduces the turn-around time, enabling high throughput processing of samples for clinical analysis and large scale genomics studies.
PMCID: PMC4162240
2.  Discovering the RNA Transcription Landscape using Directional Approaches 
High-throughput complementary DNA sequencing (RNA-Seq) is a powerful technique that allows for sensitive digital quantification of transcript levels. Moreover, RNA-Seq enables the detection of non-canonical transcription start sites and termination sites, alternative splice isoforms and transcript mutation and edition. Standard “next-generation” RNA-sequencing approaches generally require double-stranded cDNA synthesis, which erases RNA strand information. In this approach, the synthesis of randomly primed double-stranded cDNA followed by addition of adaptors for sequencing leads to the loss of information about which strand was present in the original mRNA template. The polarity of the transcript is important for correct annotation of novel genes, identification of antisense transcripts with potential regulatory roles, and for correct determination of gene expression levels in the presence of antisense transcripts. Our objective was to address this need by developing a novel streamlined, low input method for Directional RNA-Sequencing that highly retains strand orientation information while maintaining even coverage of transcript expression. This method is based on second strand labeling and excision after adaptor ligation; allowing differential tagging of the first strand cDNA ends. As a result, we have enabled strand specific mRNA sequencing, as well as whole transcriptome sequencing (Total RNA-Seq) from ribosomal-depleted samples. Total RNA-Seq provides a much broader picture of expression dynamics including discovery of antisense transcripts. This work presents a streamlined, fast solution for complete RNA sequencing, with high quality data that illustrates the complexity and diversity of the RNA transcription landscape.
PMCID: PMC3635307
3.  A Fast Solution to NGS Library Prep with Low Nanogram DNA Input 
Next Generation Sequencing (NGS) has significantly impacted human genetics, enabling a comprehensive characterization of the human genome as well as a better understanding of many genomic abnormalities. By delivering massive DNA sequences at unprecedented speed and cost, NGS promises to make personalized medicine a reality in the foreseeable future. To date, library construction with clinical samples has been a challenge, primarily due to the limited quantities of sample DNA available. Our objective here was to overcome this challenge by developing NEBNext® Ultra DNA Library Prep Kit, a fast library preparation method. Specifically, we streamlined the workflow utilizing novel NEBNext reagents and adaptors, including a new DNA polymerase that has been optimized to minimize GC bias. As a result of this work, we have developed a simple method for library construction from an amount of DNA as low as 5 ng, which can be used for both intact and fragmented DNA. Moreover, the workflow is compatible with multiple NGS platforms.
PMCID: PMC3635320

Results 1-4 (4)