10 02, 2017

Fingerprinting for multiplexed single-cell RNA-seq

By | February 10th, 2017|Categories: "Experimental design controls etc", "My almost"..., 10X Genomics, Methods and applications, Next-generation sequencing, Single-cell sequencing|Tags: |0 Comments

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 […]

24 03, 2014

5mC-PCR: preserving methylation status during polymerase chain reaction

By | March 24th, 2014|Categories: Methods and applications|6 Comments

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 […]

3 09, 2013

Finding your way around NGS sample prep

By | September 3rd, 2013|Categories: Methods and applications, Next-generation sequencing|5 Comments

  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 […]

29 08, 2013

Targeted RNA-seq methods are here

By | August 29th, 2013|Categories: Exomes and amplicons, Methods and applications, Next-generation sequencing|2 Comments

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, […]

21 06, 2013

A better way to analysis of tumour heterogenity

By | June 21st, 2013|Categories: Methods and applications, Next-generation sequencing|0 Comments

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. […]

15 06, 2013

5hmC on Illumina 450k’s: analysis without breaking the bank?

By | June 15th, 2013|Categories: Methods and applications, Next-generation sequencing|0 Comments

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 […]

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