Genomics and Epigenetics
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…
Read MoreGet 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…
Read MoreCRISPR-Based Activation (CRISPRa): A How-To Guide
CRISPRa allows you to activate or overexpress genes in a more endogenous manner. Find out the steps to getting started.
Read MoreWhat’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…
Read MoreHow to Confirm Your CRISPR-cas9 Genome Editing Was Successful
Level-up your troubleshooting ability by determining the success of failure of each stage of your CRISPR experiment.
Read MoreUse 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…
Read MoreReducing 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,…
Read MoreHow 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…
Read MoreGenerating 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.…
Read MoreBattle 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…
Read MoreAnalyzing 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…
Read MoreKick-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…
Read MoreStudying 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…
Read MoreUsing dbSNP and ClinVar to Classify Gene Variants
As we discussed previously, the gaps in our understanding of the human genome make variant classification an extremely difficult job. However, with each passing day our knowledge increases, and the tools to help us become increasingly more efficient. Let’s pick up where we left off in our first article about variants. After checking Ensemble to…
Read MoreChIP-seq Workflows Run Best with Automated DNA Size Selection
Chromatin immunoprecipitation sequencing, better known as ChIP-seq, is a massively parallel approach for understanding the interactions between proteins and DNA. This is especially important for determining the activity of transcription factors, which is why it’s frequently used to learn about the complicated series of biological steps leading to cancer. It’s also key to many epigenetic…
Read MoreDiscovering PARP inhibitor resistance mechanisms using genome-wide and focused CRISPR screens
Discovering PARP inhibitor resistance mechanisms using genome-wide and focused CRISPR screens In this webinar, Dr. Stephen Pettitt explains how he applies genome-wide targeted mutagenesis screens to elucidate the genetic basis of drug resistance. Using mouse and breast cancer cell lines, Dr. Pettitt’s team developed a targeted, genome-wide mutagenesis screen to identify mutations responsible for resistance…
Read MoreCommon challenges and solutions in microbiome analysis workflows
Common challenges and solutions in microbiome analysis workflows Elucidating meaningful, unbiased microbial community profiles from complex microbiome samples is challenging.In this tutorial, you will find: the sources of bias throughout the microbiome analysis workflow practical solutions for troubleshooting your techniques new technologies to achieve the most representative and unbiased microbiome profiles Speakers Sven Reister, Ph.D.PCR…
Read MoreGenerating High-Quality Genome Assemblies from Metagenomic Sequencing
The decreasing costs in genomic sequencing over the past decade have inspired researchers to apply shotgun next-generation sequencing to entire microbial communities. While the reads generated typically cannot be assembled cleanly into individual genomes, there is often enough information produced to identify most microbes present in the population. However, this approach lacks sufficient resolution to…
Read MoreA Beginner’s Guide to Single-Cell RNA Sequencing
Since our early steps in Science we have been told that every cell in our body has the exact same genetic information (minus one or two alterations). Therefore, the great variety of cells in our body comes from gene expression – each cell must express one set of genes and repress another set to function…
Read MoreSimultaneous Proteomics and Transcriptomics: The Future of Single Cell Analysis
Simultaneous Proteomics and Transcriptomics: The Future of Single Cell Analysis Join us in this webinar featuring Dr. Marlon Stoeckius as he explains how you can improve your single-cell RNA-sequencing (scRNA-seq) experiments.In this tutorial, you will find: How you can run one scRNA-seq experiment with numerous protein markers in parallel How you can increase your recovery of…
Read MoreGet to Know Your Reference Genome (GRCh37 vs GRCh38)
Whether your experiment relies upon a reference-based genome assembly or mapping reads to a reference genome to identify variants, you need to choose a human reference genome assembly. But wait! You go to the FTP site of NCBI’s refseq and click on the Homo sapiens folder. There you are presented with two choices. Which one…
Read MoreCRISPR-Inspired Method Targets Large, Repetitive DNA Elements
Target capture through PCR has been a mainstay in genomics for years, but scientists working on especially repetitive, poorly characterized, or rapidly evolving regions continue to struggle to fish out those stretches of DNA for further study. However, whole genome sequencing, the only other alternative for these regions, can force researchers to pay for much…
Read MoreLong Adapter Single Stranded Oligonucleotide (LASSO) Probes for Massively Multiplexed Cloning of Kilobase-Sized Genome Regions
In this webinar, you will learn how to solve a major problem in creating expression libraries from genome sequences for downstream analyses. Specifically, you will learn: The difference and benefits of LASSO cloning over NGS How LASSO cloning allows for the multiplex cloning of large open reading frames (ORFs) of bacterial, human, and human-microbiome genomes…
Read MoreDe Novo DNA Sequencing and the Special k-mer
The technology for DNA sequencing was developed back in 1977 thanks to Frederick Sanger. It took a bit longer before it was possible to sequence a complete genome. This is because we needed an appropriate mathematical model and massive computational power to assemble millions or billions of small reads to a larger complete genome. Today’s…
Read MoreA Crash Course in BLAST Searching
Simple BLAST searching is pretty straightforward to many of us. Just plug in your sequence, select the species genome, and hit search! But have you ever wondered what it takes to run a BLAST query using these mammoth-sized (no pun intended!) sequence databases? BLAST searching can produce dozens, hundreds, or even thousands of candidate alignments.…
Read MoreHow to Use Ensembl to Classify Gene Variants
Even though our knowledge about genomes grows daily, and in huge leaps, we sometimes need to remind ourselves that DNA was first isolated in 1869 and its molecular structure was only identified in 1953. The PCR reaction only hit the scientific community as recently as 1983! So even though we are growing fast, we are…
Read MoreUnderstanding and Designing Flanking Homology DNA Assembly Experiments
Understanding and Designing Flanking Homology DNA Assembly Experiments Join us in this webinar on demystifying DNA assembly.In this tutorial, you will find: How flanking homology DNA assembly methods work How to use web-based software to design experimental methods for flanking homology DNA assembly methods How synthetic DNA fragments fit in to the DNA assembly process…
Read MoreWhy You Should Use Cas9 Ribonucleoprotein Transformation for CRISPR Genome Editing
Imagine directly creating a mutation at (almost) any site in your target genome instead of screening thousands or millions of random mutants! The CRISPR/Cas9 system does just that. In its traditional form, this forward genetics approach takes 7 steps from start to mutated genome. However, there is a way to obtain your designer genome in…
Read MoreThe Good, the Bad and the Expensive of Whole Genome Sequencing
Whole Genome Sequencing (WGS) is still very cutting edge, sequencing technology and while there are a lot of perks to using it, there are also a few drawbacks. The good, the bad and the pricey are outlined below to help you navigate when it’s worth using WGS! Whole Genome Sequencing: The Good Lots of Data…
Read MoreNext Gen Sequencing Challenges
Next generation sequencing opened the doors to our genome. It gives massive amounts of information in a week – whereas Sanger sequencing takes thrice as long, and causes lab lesions due to the abusive use of pipettes. Indeed, with minimal hands-on procedures we obtain a lot of data. But nothing in Science is ever easy.…
Read MoreDNA Extraction from FFPE Tissues for NextGen Sequencing
Rapid genomic analysis offered by next generation sequencing (NGS) is ideal for personalized medicine approaches to clinical genetics, microbiological profiling, and diagnostic oncology. Many standard clinical samples are preserved as formalin-fixed, paraffin-embedded (FFPE) tissues, which presents obstacles for use in NGS analysis. FFPE tissue preservation has the benefit of keeping samples intact for histological examination…
Read MoreBest Practices for DNA Shearing for NGS
Construction of high-quality sequencing libraries is pivotal to successful NGS, and DNA quality is one of the most critical aspects of library preparation. As this Nature Methods paper illustrates, DNA shearing involves appropriate and consistent fragment sizes for sensitive and accurate sequencing, and the fragments must be accurately analyzed prior to sequencing to measure molarity…
Read MoreCodon Optimization 101
The intriguing thing about protein expression is that the combination of transfer RNAs (tRNAs) that translate the 3 letter codon into an amino acid (aa) far exceeds the number of existing amino acids (aa). If you do the math correctly, the maximum number of unique combinations using the triplet code to code for the 4…
Read MoreMaxam-Gilbert Sequencing: What Was It, and Why It Isn’t Anymore
In the mid-1970s, two methods were developed for directly sequencing DNA: the Maxam-Gilbert sequencing (or chemical sequencing) method and the Sanger chain-termination method. Indeed, in 1980, both Walter Gilbert and Frederick Sanger were awarded The Nobel Prize in Chemistry for “their contributions concerning the determination of base sequences in nucleic acids”. Actually, each got a…
Read MoreAn Introduction to Nanopore Sequencing
DNA sequencing is the most powerful method to reveal genetic variations at the molecular level, leading to a better understanding of our body in physiological settings, and pathological conditions. It is the beginning of the long road towards better diagnostics and personalized medicine. Even though there have been great advances in DNA sequencing technologies there…
Read MoreA Crash Course in CRISPR-Cas9 Editing in Drosophila
Get tips and tricks for performing CRISPR-Cas9 editing in Drosophila.
Read MoreHow to Design a CRISPR Cas9 Experiment and Start Genome Editing
Designing a CRISPR experiment can be daunting. We’ve got tips and pointers to help you get off on the right foot.
Read MoreNGS-Based HLA Typing Delivers More Comprehensive Information
Used for matching organ transplants to donors and other applications, human leukocyte antigen (HLA) typing is rapidly shifting from older methods to NGS technologies. This is a major step forward, as more complete views of the highly polymorphic HLA genes provide a deeper understanding of how a person’s natural genetic variation might affect transplant matches…
Read MoreHow to Test the Efficiency of your sgRNA
To successfully edit your genome of interest, one critical step is to test the sgRNA you have designed. Fortunately there are programs that have been developed such as CRISPRscan for zebrafish, SSC, Sequence Scan for CRISPR, or WU-CRISPR that you can use to predict the efficiency and the suitability of the sgRNA. However, the prediction…
Read MoreMeeting the BioPython
The Biopython Project is an amazing initiative that helps scientists use Python for bioinformatics – and it’s exceptionally easy to learn! You can access online services, parse (read) different file types, analyze, and do a bunch of fun stuff with your data with Biopython. The people behind the project have put in a lot of…
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