Online Learning Resources for Scientists Working From Home

Online Learning Resources for Scientists Working From Home

From bad weather to rail strikes or global pandemics, there are several reasons you may find yourself working from home. After writing up any outstanding grant proposals or papers, reviewing the literature, and perusing the endless field of coronavirus news updates, what’s a scientist to do? Brush up on your non-lab skills, of course! We…

Analyzing RNA-Seq Data
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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…

The qRT-rtPCR Control You Should Be Doing, But Probably Aren’t

The qRT-rtPCR Control You Should Be Doing, But Probably Aren’t

Every man, woman, and dog is doing quantitative real time reverse transcriptase PCR (qRT-rtPCR) these days. It’s a great method to measure your favorite transcript’s expression levels. One of the big plusses (like the Swiss flag!) of quantitative PCR in general is its high sensitivity. In principle, it can detect and quantify one molecule of…

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

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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Data Analysis for Three-dimensional Volume Scanning Electron Microscopy

In recent years, three-dimensional (3D) scanning electron microscopy techniques have gained recognition in the biological sciences. In particular, array tomography, serial block face scanning electron microscopy (SBFSEM) and focused ion beam scanning electron microscopy (FIBSEM) (described in Three-Dimensional Scanning Electron Microscopy for Biology) have shown an increase in biological applications, elucidating ultrastructural details of cells…

Introduction to Linux for High-Throughput Sequencing Analysis

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…

A Simple Method for Measuring Intracellular Fluorescence

A Simple Method for Measuring Intracellular Fluorescence

Fortunately for microscopy users, measuring intracellular fluorescence has been made relatively simple through an ImageJ plugin called the Cell Magic Wand. For those of you unfamiliar with ImageJ, it’s a popular image processing program that runs on Mac, Windows, and Linux. How to use ImageJ for measuring intracellular fluorescence First of all, to begin measuring…

Flow Cytometric Apoptosis Assays for Cell Death
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Flow Cytometric Apoptosis Assays for Cell Death

Apoptosis, often called programmed cell death, is a carefully regulated process that is part of normal development and homeostasis. Apoptosis is morphologically and biochemically distinct from necrosis, which is conversely called accidental cell death. Dysregulation of apoptosis is implicated in disease states such as cancer, autoimmune disease and degenerative conditions. Apoptosis consists of an orderly…

Top 5 Tricks for Using FlowJo

Top 5 Tricks for Using FlowJo

Are you planning to do cellular immunology research?  Then chances are you will be introduced to the flow cytometer –  “a modern immunologist’s best friend.” This modern magic box is a highly versatile machine packed with cutting-edge fluidics and photonics (lasers). Combined with the monoclonal antibodies conjugated to fluorochromes capable of emitting light signals from a…

RNA-seq: The Challenges to Diving Right In

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…

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

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…

Choose the Statistical Package that Will Make Your Data Talk

Choose the Statistical Package that Will Make Your Data Talk

In the last years, the need for using statistical testing in bioscience has grown exponentially and so has the development of statistical software. It is now common that everyone is using some sort of stats in their basic research. Among the skillful biostatisticians, R is the most popular software for data analysis, but not all…

Using a Genome Viewer to Scope your Sequencing Data

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…

Remote Cytometry: Help from beyond!

Remote Cytometry: Help from beyond!

The idea of accessing one computer from another is long established. Unfortunately, we often have visions of hackers sneaking in and stealing our data when we have most to lose. However, this type of technology can aid us in a lot of applications and to those of us who work in cytometry the benefits are (somewhat) clear. No More ‘Fail’ Moments Many researchers know the dread of…

Get Your Single Nucleotide Polymorphisms Straight From the Oven!

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…

How to Start Using Coding to Automate Image Analysis Part 1: The Simple Process

Pat yourself on the back, you saw a post with the word “coding” in the title and you didn’t freak out or glaze over. That’s the first step. Coding seems to have such a stigma attached to it; people tend to think that it’s incomprehensible nonsense that they could never learn, and that it has…

How to Start Using Coding to Automate Image Analysis Part 2: Batch Processing Multiple Images

How to Start Using Coding to Automate Image Analysis Part 2: Batch Processing Multiple Images

In Part 1 of this article, I introduced you to using code for basic image manipulation in ImageJ and working with the command recorder to expand your coding vocabulary. I covered how to make a simple macro, how to edit it and then save it to be run again another time. If you skipped the…

Multifocal Structured Illumination Microscopy: The Fast Food of Super-Resolution Techniques

Multifocal Structured Illumination Microscopy: The Fast Food of Super-Resolution Techniques

While most of us have heard of super resolution microscopy, many of you may not have heard of MSIM, or Multifocal Structured Illumination Microscopy. This under-the-radar imaging technique is relatively quick, cheap (by comparison) and will allow you to get a lot of data, fast. So What is MSIM Anyway? MSIM, as I mentioned earlier,…

How to See the Cell Cycle Through Your Microscope

How to See the Cell Cycle Through Your Microscope

Even in the most basic applications, fluorescence microscopy can be a very powerful technique. Simply put, the ability to actually see the biology you are interested in cannot be matched in directness. Often, the aim of fluorescence microscopy is to observe the effect of an experimental manipulation. Ultimately, you would like to know that the…

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

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…

Branching Out – 5 Steps to Creating a Phylogenetic Tree

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…

Free Resources for Teaching Yourself to Analyze Next Gen Sequencing Data

Free 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…

Pathway Analysis for Next Gen Data

Pathway 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…

Roadside Assistance: Fixing Your Broken-Down ELISA

Roadside Assistance: Fixing Your Broken-Down ELISA

The ELISA (enzyme-linked immunosorbent assay) is arguably one of the most important and versatile tools in the toolbox of molecular biologists, biochemists and diagnosticians across the world. Defined by its simplicity and speed, the assay is easy to learn and perform in as few as five steps. But with so few variables to manipulate, an…

How to Make Sure Your NGS Results are Robust

How 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…

Data Spread and How to Measure It: the Coefficient of Variation (CV)

Data Spread and How to Measure It: the Coefficient of Variation (CV)

No matter how we make measurements, there will be variation (a spread of data). Take 100 people and ask them to guess your age and you will get a range of results: some will be too low (excellent!), some too high (not so good!). It is the same with any of our laboratory experiments –…

Top Resources for Learning a NGS Programming Language

Top 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…

Choosing a Scripting Language for Next Generation Sequencing: Python, Perl, and More

Choosing 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…