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Genomics and Epigenetics

Guide to CRISPR/Cas9 Delivery: How to Maximize Your Editing Efficiency

In this webinar, you will learn how to maximize your genome editing efficiency using CRISPR/Cas9 and how to apply this technique in your research. The main points in the webinar will include: How to design guide RNAs using online tools specific to the genome and application of interest. Tips and practical advice to assist you…

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Demystifying NGS: Depth Coverage and Deep Sequencing

NGS is not a three-headed monster. However, it can be a difficult concept to grasp—especially when you are getting started.  There is a lot of new terminology, and a whole new world to discover: both in the lab bench and in interpreting your results. It helps to start somewhere. So, let’s start! Depth of Coverage…

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A Primer on Checking the Methylation State of the Genome

We all know that genes encode proteins that make up a living cell. However, the level and coordination of gene expression is really the key to the success of a living cell. One way eukaryotic cells (that’s us!) control protein expression is through addition of a methyl or hydroxymethyl group on the cytosine nucleotide. This…

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Show Disparity in Gene Expression with a Heat Map

Have RNA-seq or microarray data? What possible tools can help you find your genes of interest? Is there any pattern in your expression data? I know you are totally at sea but heat maps are now commonly used to help. A heat map is a well-received approach to illustrate gene expression data.  It is an…

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Phylogenetic Tree Construction Made Easy with Blast & Mega

Your DNA sequence can be put to good use fairly easily with Blast and Mega software. These programs can help in phylogenetic tree construction. You can ask questions like what is the evolutionary relationship between a set of sequences from different species? Or how have certain microbial strains arisen? Blast As any bioscientist probably knows,…

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How to Generate High-Quality SNPs Data Sets from NGS

SNPs or single nucleotide polymorphisms are on many scientist’s wish list in experimental studies of genomic DNA sequences. Methods to detect SNPs have evolved. Now with the availability of high throughput sequencing methods, also known as next generation sequencing (NGS), SNPs can be identified in the large amounts of DNA sequence that is generated. There…

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Investigating an Expression Quantitative Trait Locus (eQTL)

Thousands upon thousands of genetic variants are now associated with every disease and trait you can possibly think of. Such traits range from cancers to blood pressure, intelligence, height, weight… and many more! This is largely because of the advent of genome-wide association studies (GWAS). However, the vast majority of genetic loci associated with these traits are…

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Variations on the ChIP-seq Theme and Challenges of Befriending Large Datasets

ChIP-seq has proved amazing. Through these new techniques, we can obtain big datasets in a matter of days, making our lives in the lab easier and more efficient. ChiP-seq combines chromatin immunoprecipitation (ChIP) assays with whole genome sequencing. This makes it possible to understand where proteins bind to DNA and epigenetic modifications. Humans are not only their…

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Genomics Software – Doorways to Visualize Sequence Data

Are you tired of staring at all of your sequence data? Want to know the easiest way to look at it? For complex genomics data, an appropriate visualization tool is a must have. The right genomics software will make it easy-peasy to get some results as well as test all those ideas you have. Since…

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Introduction to Linux for High-Throughput Sequencing Analysis

So, you’ve spent time planning your high-throughput sequencing experiment. You’ve chosen how many replicates to use, deliberated about sequencing depth, and kept everything RNase-free. Now you have many gigabytes of data available. What’s next? While the first step of RNA-Seq analysis is aligning your sequencing reads to a reference genome, first you need to get…

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How to Follow up on a GWAS (Genome-Wide Association Study)

So, the genome-wide association study (GWAS) data for your disease of interest was published, and it has thrown up some very interesting associations. However, at this stage, bear in mind that this is only an association. Your project is to provide the link between the GWAS single nucleotide polymorphisms (SNP) and pathological changes. Where do…

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How Does Automated Electrophoresis Perform DNA Size Selection?

Anytime lab processes get automated by a sophisticated scientific instrument, there can be a “black box” effect, leading users to wonder what’s going on in there. For DNA electrophoresis, it’s no different. It’s easy to see what’s happening in a manual gel, but the automated gel-based DNA size selection platforms can be more mysterious. Automated…

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An Introduction to Shotgun Sequencing: Fire in the Hole

In the midst of all the cool new sequencing techniques and technologies out there today, you may have overlooked the tried and true method of Shotgun Sequencing. What is Shotgun Sequencing Anyway? Shotgun sequencing gets its name from the concept that a large sequence is essentially broken up in to many, many smaller pieces, similar…

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How to Choose The Appropriate Genomic NGS Data Simulator

Let’s say that you’ve just finished gathering your NGS reads and you’re going to simulate the introduction of random mutations at specific rates into the reads. Before you move on to the next step, you need to determine which NGS data simulator will get the job done. With the ever-increasing advancement of NGS in the…

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P19 to the Rescue: How to Increase Protein Expression in Agroinfiltration

Plants are just not green gods—they can be more. You can cost-effectively express your recombinant complex proteins in a plant system. More interestingly, plants are ideal systems for producing functional monoclonal antibodies, enzymes, and vaccine components! They can also be used for protein localization studies. To save time, you can transiently express your protein using…

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DNA Sizing Tutorial: When to Use Manual Gels, Beads, and More

There are several methods for size-selecting DNA fragments prior to sequencing. How do you choose which is best? Here’s a look at various options, plus considerations to help you determine when to use each one. Manual Gels Virtually every student in a biology lab knows how to prepare and cut a manual gel—but their ubiquity…

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The Ins & Outs of Illumina Sequencing

The future of personalized medicine depends on affordable DNA sequencing. In the race for the $1,000 genome, several sequencer manufacturers are working on making equipment that can sequence DNA and RNA faster and more accurately. But so far, only one company – San Diego, California-based Illumina – has US FDA regulatory approval to use its…

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RNA-seq: The Challenges to Diving Right In

It’s the hot new technique. With a single procedure, you can get information about all RNA transcripts at once! It sounds like a dream. While RNA sequencing (RNA-seq) has opened the door to exciting new questions, scientists interested in pursuing this technique should be aware of the roadblocks ahead of them. While RNA-seq can be…

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For Better NGS Assemblies, Use More Precise DNA Size Selection

It may not be intuitive that a sample preparation step like DNA size selection would have a significant impact on downstream data analysis, but NGS users have proven that it does. Indeed, the precision of your size selection (or lack thereof) can make or break a genome assembly. Consider the alignment challenge for paired-end reads:…

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All about miRNAs: Practical Tips, Advice, and Applications

In this webinar you will learn the tips and tricks necessary for you to successfully work with miRNAs, and how you can use them to further your research. The main points we will cover are: Tips and practical advice to help you work with miRNAs, including isolation and delivery The biology and mechanism of miRNAs and…

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Where Did It All Go Wrong?! Quality Control For Your NGS Data

You’ve carefully collected your samples, extracted nucleic acids and made your first set of next-generation sequencing libraries. How are you going to know if the data you get back is any good and whether it will be worth the effort in learning how to do the analysis? Who is to blame? Fortunately, there are several…

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Breaking Down the Assembly of Nucleic Acid Sequences

Microbiome—a term that has become a hot topic in recent years—has scientists of all disciplines wanting to know more. Microbes are everywhere. On any type of surface you can think of. Our physical make up, by number, consists of 10 bacterial cells to every one of our own. What’s more, approximately 99% of microbes cannot…

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Sanger Sequencing: How the Genome Was Won

I’ve never run a sequencing gel in my life, but people around me did, and they spent a lot of time on getting it just right. Although the principle described by Sanger in 1975 sounds straightforward (1), sequencing gels are very long and very thin – less than a millimeter thick! They were easy to…

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Kiss your samples goodbye: Outsourcing your Next-Gen experiment

Genomic Science has come a long way since the early days of Sanger sequencing in the 1970’s. Today, there are jazzy new sequencing technologies that include fragment analysis, epigenetic sequencing, RNA/transcriptome sequencing and Next Generation Sequencing (NGS). Increasingly these technologies are becoming more accessible, but they still require highly specialized (read: expensive) equipment. Unless your…

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Get Started in Genome Editing with CRISPR

The development of CRISPR/Cas9 technology has made it relatively straightforward to selectively edit genomes and has revolutionized the way in which we approach biological questions. CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats and in simple terms, this technique allows you to direct a nuclease to cut at a specific site in the genome of interest. The…

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Want NGS Success? Consider These Three Factors

NGS is still something a little scary for most operators. Mainly because of the price, which can make the pipette, in the hand of the best of us, shake a little with fear. And even though the protocols have a tendency for getting simpler, faster, and more appropriate for a routine, there are still crucial…

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Get Your Single Nucleotide Polymorphisms Straight From the Oven!

While it is true that there are some useful websites like SNPedia, or NCBI that can help you find rs codes for genetic variants, sometimes you need that info coming straight from the oven – particularly when you want to look at atypic SNPs or substitutions that have not been validated. So, in this post I…

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Navigating the Sea of Human Genetics, Part I

Ahoy mateys! At my workplace we’ve recently become EXTREMELY excited about a resource called the HuGE Navigator. It’s so great that it’s going to take me a couple of articles to highlight its features. Hop on board to learn a little about it! So What is HuGE Navigator? HuGE Navigator is an integrated set of…

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Using a Genome Viewer to Scope your Sequencing Data

Now you’ve got great sequencing results, thanks to Nick’s article on improving sequencing results. Now what? Well now you need some software (preferably free) to analyze your data. BioEdit is a good option. But what I have to offer today is a much lighter and equally handy tool. It’s called Artemis and was developed by…

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Mysterious Plant miRNAs: What About Them?

Welcome to the last article in this series! Last, but by no means least, we will look at the importance of plant miRNAs and how they differ from their animal counterparts. When/How Were Plant miRNAs Discovered? Plant miRNAs were first described in 2002, a decade after the seminal miRNA study in the nematode C. elegans…

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Omics Software Galore!

If you are looking for Omics software, then I suspect the G6G Directory of Omics and Intelligent Software need be your only stop. From the name it will come as no surprise that this website is a directory of Omics and AI software. On the Omics side it lists software for: Genomics Gene Expression Analysis/Profiling…

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An Introduction to RNA-seq

RNA sequencing (Wang 2009) is rapidly replacing gene expression microarrays in many labs. RNA-seq lets you quantify, discover and profile RNAs. For this technique, mRNA (and other RNAs) are first converted to cDNA.   The cDNA is then used as the input for a next-generation sequencing library preparation. In this article, I’ll give a brief…

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Nanopore Sequencing: An Update

People would have said that a USB sequencer not much bigger than a memory stick which could sequence genomes in 50kb+ read-lengths was impossible “’Star Trek’ technology!” Now, that futuristic technology is here.

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Single Molecule Real-Time Sequencing

Recently, I have witnessed the uprising of various next generation sequencing (NGS) platforms and it’s quite interesting because each platform uses a different method. Previously, I’ve written about the exciting possibility of nanopore sequencing—a new sequencing technology based on the “signature” electrical currents generated as a single strand of DNA passes through the nanopore. The…

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Learn-omics! What is that “Omics” I keep Stumbling Upon?

Genomics, transcriptomics, proteomics, metabolomics – words that in 2015 sound very familiar even to a freshman in any biology field. Although most have heard those words before, I keep encountering students or even post-graduates who find it difficult to explain what they are. So, to make things easier here is a peek behind the curtains…

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How to Express Proteins Across Kingdoms: Prokaryotes vs Eukaryotes

In the sci-fi novel Terminal World by Alistair Reynolds, a planet consists of zones with defined characteristics of matter interactions on a subatomic level. These conditions permit different levels of technology sophistication in various zones. For example, in the “Steamville zone” nothing more complicated than steam engines works – electronic schemes fuse irreversibly. Something like…

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How To Analyze Your Single Nucleotide Polymorphism (SNP) Chip Data

So, you’re sitting there with your list of significant SNPs, thinking, “what do I do now”?  Hopefully this article can point you in the right direction! So far, you will have extracted genomic DNA from your organism of interest, sourced the SNP chips required, and had the DNA run on these chips.  The chips will…

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