James Hadfield's Profile

read on

An Introduction to RNA-seq

RNA sequencing (Wang 2009) is rapidly replacing gene expression microarrays in many labs. mRNA (and other RNAs) are converted to cDNA that is used as the input to a next-generation sequencing library preparation. RNA-seq allows you to quantify, discover and profile RNAs. In this article, I’ll give a brief review of RNA-seq and introduce the […]

read on
In Genomics & Epigenetics 9th of July, 2016
nanopore sequencing read on

Nanopore 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 on
In Genomics & Epigenetics 9th of July, 2016
read on

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 […]

read on
In Genomics & Epigenetics 9th of July, 2016
read on

Why 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 on
In Genomics & Epigenetics 16th of July, 2015
read on

Quantifying 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 on
In Genomics & Epigenetics 20th of February, 2015
read on

Top 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 on
In Genomics & Epigenetics 2nd of January, 2015
read on

The Real Cost of Sequencing in 2014

We are now living in the era of the $1000 genome. Unfortunately, most of us are still paying significantly more than this for a genome, or an equivalent amount of data in the form of exomes or RNA-seq reads. There are several reasons for this higher-than-expected price and this post aims to highlight where the […]

read on
In Genomics & Epigenetics 5th of December, 2014
read on

The Birth Of The Epitranscriptome: RNA Gets Methylated Too!

Most biologists are aware of chemical modification of DNA in the form of 5-methylcytosine (mC), the eponymous ‘5th base’. Moving to the 6th base The fields of epigenetics and epigenomics are increasingly having an impact on our understanding of biology and a subsequent impact on medicine. Some biologists are aware of the wider range of DNA […]

read on
In Genomics & Epigenetics 17th of October, 2013
DNA shearing read on

Shearing DNA For Next Generation Sequencing: Which Method Should I Choose?

Next-generation sequencing (NGS) really has taken the world by storm! In NGS, millions of short ‘read’s are sequenced in a short space of time, leaving you with vast amounts of data to analyze! For all NGS platforms, the input sample (i.e. your cell free DNA) must be cleaved into short sections or fragments prior to […]

read on
In Genomics & Epigenetics 20th of June, 2013
read on

Why 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 on
In Genomics & Epigenetics 2nd of May, 2013