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Genomics & Epigenetics

2015 Staff Picks: Next Generation Sequencing

Celebrate the coming New Year with what’s next: Next Generation Sequencing. Our stunning (and wildly intelligent—if I do say so myself) editorial team picked out our favorites from the past year. We hope that you find them as interesting and helpful as we do!   Jen Redig, Managing Editor Free Resources for Teaching Yourself to…

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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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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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Branching Out – 5 Steps to Creating a Phylogenetic Tree

Welcome to the magical world of systematics! Looking for a way to produce a phylogenetic tree that’s a step above the default options, time efficient, not too program heavy and avoids using command line programs? Although there are more rigorous analyses that strict systematists perform, for your purposes, the following should suffice. 1.  Data selection…

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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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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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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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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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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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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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Controlling Gene Expression with CRISPR Interference (CRISPRi)

The genome editing technology, CRISPR/Cas9, is well known for assisting researchers in manipulating the genome of target cells and has already been discussed in a few posts. This article is about repurposing the typical genome editing technology to interfere with gene expression, known as CRISPR interference (CRISPRi). The purpose of CRISPRi is regulation of the…

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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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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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The Art of Size Selection for Small RNAs

Size selection is a critical step in NGS pipelines, but may be most challenging for studies of small RNAs. The concept behind size selection is simple: separate a sheared DNA or cDNA sample by fragment size, and then use the resulting sizes to remove unwanted fragments. This is a tried-and-true way to get rid of…

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For Long-Read Sequencers, Size Selection Is Key

It took scientists a little while to warm up to long-read sequencing, but now you couldn’t pry most of them away from their sequencers with a crowbar. Long reads — we’re talking 10,000 bases and more — provide a level of contiguity and completeness in genome assemblies that simply isn’t possible with short-read sequencers. They…

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Decoding the Genome: Applications of DNA Sequencing

The age of sequencing is undoubtedly upon us. From improving cancer diagnostics to pinning down elephant poaching hotspots, DNA sequencing is revolutionizing the world around us from the ground up. The latest video from Thermo Fisher Scientific’s “Behind the Bench” blog, 10 moments in DNA sequencing gives fascinating insights into the amazing advances being made…

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