Genomics and Epigenetics
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…
Read MoreSanger 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…
Read MoreWhere 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…
Read MoreUsing 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…
Read MoreAn 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…
Read MoreBreaking 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…
Read MoreGet 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…
Read MoreAnchored Multiplex PCR for Next Generation Sequencing
Anchored multiplex PCR (AMP) is a powerful method for amplifying minuscule amount of nucleic acids. Combined with Next Generation sequencing, AMP just might be what you need to identify genetic mutations.
Read MoreWant 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…
Read MoreKiss 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…
Read MoreHow 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…
Read MoreGet 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…
Read MoreSingle 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…
Read MoreMysterious 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…
Read MoreNanopore 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.
Read MoreHomology Terminology: Never Say the Wrong Word Again
I’ve noticed that there exists some ambiguity about the different terms relating to homology. I’ll try to break them down here, with significant help from Genome Biology.
Read MoreHow 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…
Read MoreNanopore Sequencing
A disruptive sequencing technology Every new generation, a new concept is born and can completely reshape the landscape of biomedical research. Nanopore sequencing technology, although still at its infancy, is beginning to look like a “game-changer.” It’s a revolutionary concept in sequencing in which strands of nucleic acids are fed through a tiny pore (nanopore)…
Read MoreAll in the Chip: Ion Torrent Sequencers
Ion Torrent technology, when it was introduced in 2010, was one of several machines that promised to revolutionize genetics. These were benchtop machines that showed their prowess in quickly sequencing smaller exomes and other DNA samples (about 10-20 million bases per run, compared to Illumina HiSeq, which could read 250 billion bases in a run).…
Read MoreLearn-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…
Read MoreThe 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…
Read MoreFor 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…
Read MoreDecoding 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…
Read MoreWhy DNA Size Selection Matters in NGS Pipelines
Of all the sample prep steps necessary for next generation sequencing, DNA size selection may have the greatest impact on quality of results. After all, ineffective sizing can waste sequencing capacity on low molecular weight material such as adapter-dimers or primer-dimers, while imprecise sizing can prevent bioinformaticians from producing accurate assemblies. High-quality size selection can…
Read MoreAdventures in Genomics: Single-Cell Sequencing in Cancer
Do you want to know more about the story behind some of today’s big developments in sequencing technology? Illumina recently started a video series called “Adventures in Genomics” that introduces the people working on methods and applications, making big waves in our understanding of science, biology, and medicine. The company’s most recent video covers single-cell…
Read MoreWhy Is It Important To Run Your NGS Gels Consistently?
This article discusses some of the important things to consider if you are using agarose gel electrophoresis for size-selection of your NGS libraries. Gel electrophoresis is a simple and very commonly used technique in most labs. Careful! It’s a critical step However this simplicity means people can often overlook the fact that there are applications where…
Read MoreFree Resources for Teaching Yourself to Analyze Next Gen Sequencing Data
If you’re new to next gen sequencing, figuring out what to do with your results can be a daunting process. Luckily, you’re not alone—plenty of people have been in your shoes, and there is tons of information about data analysis out there. Here are some free resources you can use to get up to speed…
Read MorePathway Analysis for Next Gen Data
Squinting at a long list of significant genes from your latest RNA-seq experiment? Having trouble making sense of the results? You’re not alone. Pathway analysis is becoming increasingly popular because it helps researchers make sense of complex data sets, including those obtained using next gen sequencing techniques. By systematically culling information about biological pathways and…
Read MoreHow to Make Sure Your NGS Results are Robust
Next gen sequencing is a powerful technique, one that now lies at the heart of many scientific projects. This power comes with some special challenges, however, and by recognizing them you can ensure that your NGS results are robust. No one wants to publish findings that other scientists fail to replicate, but unfortunately it happens…
Read MoreGeneDig: An Easy-to-use Genome Browser for Bioscientists
The recent advancement of next generation sequencing technology and the development of novel gene editing tools, such as CRISPR-Cas9, have revolutionized research in genetics. In this golden era of molecular biology, knowing how to dig and navigate through all the enormous sequence information is an essential skill for most molecular biologists. However, to obtain facile…
Read MoreGenomic Analysis of Single Cells: The Benefits of Being Single
You don’t need to be told about how next generation sequencing technologies have revolutionized the way we study the genome and the epigenome. Whether you want to look at transcription (RNA-seq), translation (Ribo-seq) genomes (DNA-seq), interactions of proteins and DNA (ChIP-Seq) or to study epigenetic features such as methylation (whole genome bilsulfite sequencing) there are…
Read MoreFrom ChIP-seq to MeDIP: A Glossary of Different NGS techniques
It was not long since the commercialization of NGS (a little more than ten years ago) that scientists went beyond the basics and got creative with the new technology to study much more than just the sequence of DNA. In this article we highlight some of the different NGS technologies and methods available out there.…
Read MoreA Quick-Fire Guide to Shotgun Sequencing (and Assembly)
“Making the simple complicated is commonplace; making the complicated simple, awesomely simple, that’s creativity.” – Charles Mingus Next Generation Sequencing (NGS) technology has boomed in recent years, allowing researchers to probe further into the workings of the genome. According to the theory of simplicity, it is the simple principles on its basis that make…
Read MoreQuantifying Your NGS Libraries
If you want to get the maximum yield and quality from your next-generation sequencing experiment then you are going to need to make sure each of the libraries you produce is carefully quantified ready for pooling and/or loading onto a flow cell. If the quantification goes wrong you’ll get a bad balance of samples within…
Read MoreTop Resources for Learning a NGS Programming Language
In my previous article ‘Choosing a scripting language for next gen sequencing: Python, Perl, and more’ I discussed several of the more common programming languages used for next generation sequencing and things to consider when picking which one to learn. But now that you know WHAT you want to learn, HOW do you go about…
Read MoreChoosing a Scripting Language for Next Generation Sequencing: Python, Perl, and More
Large amounts of data? Check. Repetitive tasks? Check. If you work with next gen sequencing data, you have probably already realized it’s a good idea to learn a scripting language. But learning a programming language is a major endeavour, and with lots of languages available how do you decide which one to study? And once…
Read MoreTop 10 Tips for NGS Library Preparation
Making a Next Generation Sequencing (NGS) library can seem a bit daunting to the new user, as failures can be expensive. But don’t be put off, as NGS library preparation is relatively simple molecular biology, and can be very easy if you choose to use a commercial kit from one of the many suppliers. Take…
Read MoreSaying goodbye to 454: how to choose your next NGS platform
The Rise and Fall of the 454 Sequencer The GS20 454 sequencer, released in 2005, was the first next-generation DNA sequencer to hit the market, and its feats quickly dazzled the scientific community. As new sequencing platforms proliferated, however, many researchers opted for less expensive options and 454 market share fell. About a year ago,…
Read MoreA Beginner’s Guide to Next Generation Sequencing (NGS) Technology
The completion of the Human Genome Project in 2003 ushered in a new era of rapid, affordable, and accurate genome analysis—called Next Generation Sequencing (NGS). NGS builds upon “first generation sequencing” technologies to yield accurate and cost-effective sequencing results. Fred Sanger sequenced the first whole DNA genome, the virus phage ?X174, in 1977. In that…
Read MoreBeware The Bane of Batch Effects
A promising study on using gene expression to develop personalized treatments for ovarian cancer. A report of surprisingly high levels of differential gene expression among different ethnic groups. The announcement of previously unsuspected levels of physiological diversity in Plasmodium falciparum, the parasite that causes the most deadly form of malaria. What do these three seemingly…
Read More