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Genomics and Epigenetics

WGS Workflow: From Sample Collection to Data Interpretation

The efficiency of whole genome sequencing (WGS) workflows has skyrocketed since its inception. Major leaps and minor tweaks in the WGS workflow have compounded over time resulting in radical reductions in processing time and the cost of sequencing whole genomes over the past decades. The complete sequencing of the first human genome, named the Human…

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The Recipe for Successful Whole Genome Sequencing

The success of whole genome sequencing (WGS) is shown in the quick and efficient scientific response to the 2011 outbreak of E. coli in Germany and France.1 German and French strains of E. coli were indistinguishable using standard tests.  However, WGS analysis showed 2 single nucleotide polymorphisms (SNPs) in the German strains and 9 SNPs…

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CRISPR Nucleases: The Ultimate Guide To Selection

CRISPR nucleases continue to dominate the gene-editing landscape because they are powerful and easy-to-use gene-editing tools. Their rapid discovery and development, however, make choosing the right nuclease for your experiment difficult. This guide highlights the broad range of available CRISPR nucleases and distils the major factors you should consider when choosing one for your next…

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A Colorful Route to Sequencing Success

An oft-repeated maxim in biological bench science is that any experiment is only as good as its control. A control is an unchanging standard of comparison in an experiment, and an internal control is typically a standard reaction run together with the test reaction in the same reaction mixture. The purpose of an internal control…

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CRISPR Multiplexing Strategies: What’s The Choice?

Although multiplex CRISPR gene editing can be accomplished by simply introducing more than one gRNA to your target cells, there are many alternative — and more efficient — ways of achieving this goal. This article discusses these alternative CRISPR multiplexing strategies and highlights their potential caveats. Not sure whether multiplex CRISPR gene editing is right…

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DNA Extraction for Next Gen Sequencing

The advent of Next Gen Sequencing (NGS) has been truly amazing. One of the marvels that is often overlooked is how advances in DNA extraction technology have helped streamline NGS workflows. The original standard – phenol/chloroform extraction – is not well suited to the automated nature of today’s sequencing workflows (though with the emergence of…

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Get Prepped: Nanopore Library Preparation Optimization

Nanopore is a relatively new sequencing platform and researchers are still trying to optimize the protocol for their own specific applications. In our lab, we work primarily with metagenomic samples and use the 1D sequencing kits. Over the past year, we have optimized this technique. To check the quality of the Nanopore library preparation we…

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What’s that Organism? Using DNA Barcoding for Species Identification

In both the lab and field, it is important to know what species we are working with. While morphological data has always been a tried and true method of identifying species, DNA barcoding allows us to identify species when we don’t have that option (e.g. if we don’t have enough of a specimen to identify…

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Use ddRAD-seq to Study Non-Model Organisms

Reduced-representation genome sequencing has been one of the most important advances in the last several years for enabling massively parallel genotyping of organisms for which there is no reference-grade genome assembly. An implementation of the approach known as ddRAD-seq, first conceived in the Hoekstra lab at Harvard, has been widely adopted by the plant and…

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Reducing GC Bias in WGS: Moving Beyond PCR

WGS technologies have seen significant progress since the completion of the Human Genome Project in 2003. First-generation Sanger Sequencers were limited by lengthy run times, high expenses, and throughputs that read only tens of kilobases per run. The arrival of second-generation sequencers in the mid-2000s brought about the plummeting of sequencing costs and run times,…

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How to Improve Your WGS DNA Library

In whole genome sequencing (WGS) initiatives it is not enough to simply sequence the whole length of the genomic DNA sample just once. This is because genomes are usually very large. The human genome, for example, contains approximately 3 billion base pairs. Although sequencing accuracy for individual bases is very high, when you consider large…

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Generating RNA-seq Libraries from RNA

One of the most powerful methods of modern cellular biology is creating and analyzing RNA libraries via RNA-sequencing (RNA-seq). This technique, also called whole transcriptome shotgun sequencing, gives you a snapshot of the transcriptome in question, and can be used to examine alternatively spliced transcripts, post-transcriptional modifications, and changes in gene expression, amongst other applications.…

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Battle of the Methods: Whole Transcriptome Versus mRNA-seq

Maybe you want to examine the entire transcriptome or maybe you want to investigate changes in expression from your favorite gene. You could do whole transcriptome sequencing or mRNA-seq. But which one is right for your project? From budget considerations to sample collection, let’s briefly look at both to see which might be best for your…

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Analyzing RNA-Seq Data

RNA-seq is based on next-generation sequencing (NGS) and allows for discovery, quantitation and profiling of RNA. The technique is quickly taking over a slightly older method of RNA microarrays to get a more complete picture of gene expression in a cell. Data generated by RNA-seq can illustrate variations in gene expression, identify single nucleotide polymorphisms…

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Kick-Start Your Gut Microbiome Study in Four Easy Steps

Today, the gut microbiome is garnering a large amount of media attention for its role in human health and disease. From influencing immune responses to impact our brain, the gut microbiome is an important and necessary aspect of our life. So much so, that current investigations in the gut microbiome are focusing on developing biomarkers for…

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Studying the Epigenome by Next Generation Sequencing

The epigenome has been in the research spotlight, and for good reason. Not only has it been associated with the developmental stages of an organism, but epigenetic alterations lead to disorders and have been linked to many human diseases. So, the question stands: what exactly is an epigenome? What Is the Epigenome? Simply put, the…

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