In this post I describe an idea for using SNP fingerprinting for single-cell RNA-Seq to identify which sample each individual cell comes from in a multiplexed library prep. The reason for my thinking about this is that single-cell experiments are expensive. Although the cost-per-cell can […]
We do lots of DNA, RNA and NGS library normalisations mostly by hand after calculating dilutions in Excel. It works well but is cumbersome and prone to error. We’re fortunate to have an Agilent Bravo robot and are now automating more of this with excellent […]
I’m continuing a series of posts that will highlight small advances we’ve made in the lab that are unlikely to be published in their own right, this time its the turn of SPRI-bead clean-ups and how we used them to rescue some samples that would […]
Methylation analysis is hampered by the simple fact that PCR amplification removes methylation marks from native DNA. We came up with a simple idea to produce a thermo-stable DNA methyltransferase to preserve methylation status through PCR cycles, allowing amplification of DNA and simplified analysis. The […]
In a post earlier this week I talked about the hacking of a MiSeq run by MadsAlbertsen, one comment on the post drew my attention to another paper I’d missed where the authors hacked their MiSeq to perform 600bp reads (PE300). Considering this was a […]
I’ll start off by saying not quite, but you can read on to get an idea on how to increase read length of a MiSeq 500cycle v2 kit to get 600bp of data. MadsAlbertsen posted on a SEQanswers thread about their protocol to squeeze a […]
I’m often asked which sample prep method a user should consider for their experiments. In my lab we use a lot of Illumina TruSeq kits; we’ve tried other methods, and do use Rubicon’s Thruplex, but Ilumina’s end-to-end support is useful in a medium sized […]
Illumina and Life Technologies are both launching targeted RNA-seq applications which are likely to become standard tools for many labs; if the price is right. The ability to target a portion of the genome has revolutionised next-generation sequencing experiments. The analysis of exomes has exploded, […]
Ben Raphael’s lab at Brown University have just published THetA for tumour heterogeneity analysis; it’s a great paper so download it and have a look yourselves.Solid tumours have been shown to be highly heterogeneous and that this can underlie drug resistance and eventual relapse in patients. […]
Epigenetics is one of the most exciting areas of research and promises to impact all sorts of biological systems. DNA methylation has recently been shown to come in methylcytosine (mC) and 5-hydroxymethylcytosine (5hmC) flavours. Usually analysis of mC is carried out using bisulfite conversion or […]
