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Genomics and Epigenetics

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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Using 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…

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ChIP-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…

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Discovering 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…

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Common 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…

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Generating 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…

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A 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…

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Simultaneous 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…

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Get 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…

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CRISPR-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…

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Long 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…

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De 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…

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A 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.…

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How 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…

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Understanding 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…

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Why 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…

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The 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…

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Next 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.…

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DNA 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…

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Best 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…

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Codon 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…

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Maxam-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…

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An 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…

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NGS-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…

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How 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…

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Meeting 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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Probability Theory and Molecular Barcodes

In biology, a molecular barcode is a characteristic DNA sequence used to distinguish and gather together similar items. Such a simple but powerful concept is useful in various applications. As an example, the Barcoding of Life project aims to identify specimens through the sequencing of standard gene regions, and use these as barcodes. On the other…

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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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