24 11, 2017

SPLiT-Seq: single-cell RNA-Seq without the hardware

By | November 24th, 2017|Categories: Methods and applications, Next-generation sequencing, Single-cell sequencing|Tags: , , |0 Comments

I’ve been meaning to write up a post on a BioRxiv report from earlier this year: “Scaling single cell transcriptomics through split pool barcoding”1. The Seelig Lab at the University of Washington have developed a single-cell RNA sequencing method to enable labelling RNA molecules with cell-of-origin information using […]

8 11, 2017

Error-corrected ctDNA sequencing for mutation and CNV using UMIs

By | November 8th, 2017|Categories: ctDNA, Exomes and amplicons, Methods and applications, Next-generation sequencing|0 Comments

A recent BioRxiv report from the Gerlinger group at ICR describes a targeted ctDNA sequencing method that uses error correcting UMIs to achieve 100% sensitivity for mutant allele frequencies of >0.15%, and 87% at >0.075%, and reduce false-positive mutation calls by 98.6%, without adversely affecting the […]

7 11, 2017

R vs Excel by @vivalosburros

By | November 7th, 2017|Categories: I am not a Bioinformatician, Methods and applications, Other stuff|0 Comments

In this post I wanted to highlight the wonderful “Excel vs R: A Brief Introduction to R”  by Jesse Sadler. This is full of useful and practical advice on using R in place of Excel (or any other spreadsheet) for simple data analysis. I use […]

19 10, 2017

@Illumina Nextera Flex

By | October 19th, 2017|Categories: Exomes and amplicons, Library Prep, Methods and applications, Next-generation sequencing|1 Comment

My lab has been a long-time user of Illumina’s transposase exomes for the very simple reason that the 50ng input has been the lowest on the market for number of years*. This made it attractive for cancer samples where we are really limited on DNA availability; […]

16 10, 2017

WGS of HPV reveals the finer details of HPV genetic variation

By | October 16th, 2017|Categories: Methods and applications, Next-generation sequencing, Uncategorized|0 Comments

Because HPV has such a small  and relatively simple genome (8,000 bp encoding 8 genes) it is possible to screen for genetic variation that may underly carcinogenesis. A team from the National Cancer Institute (NCI) has just published the sequencing of over 5,570 human cell and tissue samples – […]

12 10, 2017

Who’s the scientific equivalent of Harvey Weinstein?

By | October 12th, 2017|Categories: Other stuff|0 Comments

The news about Harvey Weinstein can hardly have escaped the attention of even the most lab-bound post-doc ro PhD student. The investigative journalism at the The New York Times story has led to the downfall of a movie mogul for sexual harassment, unwanted physical contact and other things most of us […]

5 10, 2017

Posting Enseqlopedia content to LinkedIN

By | October 5th, 2017|Categories: Uncategorized|0 Comments

Hopefully this post is going to pop up as if by magic to all my LinkedIn contacts. This is something I’ve been meaning to do for ages and finally had a go. Thanks to the people at WPBeginner for writing this “how to guide” to make […]

3 10, 2017

Explaining rare disease during bedtime storytime

By | October 3rd, 2017|Categories: Creative, Other stuff|0 Comments

I had the very real pleasure of introducing Prof Lucy Raymond at Biotexcel’s Genomic Medicine 2017 in Cambridge last week. She was speaking in a session that included Dr David Bentley (Illumina Inc – Genomes for Medicine), Prof Stephan Beck (UCL Cancer Institute – Towards Personal Epigenomics), and Prof Sadaf Farooqi (University […]

3 10, 2017

DNA in vellum proves authenticity of paintings

By | October 3rd, 2017|Categories: Next-generation sequencing, Other stuff|0 Comments

A short article in todays Times quotes William Cowley parchment makers as saying velum provides the only foolproof way for detecting art forgery. Very simply an artist creates their work on vellum and retains a sample for genetic comparison should a suspected forgery come to […]

21 07, 2017

DAP-Seq for higher-throughput transcription factor analysis

By | July 21st, 2017|Categories: Methods and applications, Next-generation sequencing|0 Comments

The Ecker lab at the Salk Institute published a method for very high-throuphut transcription factor analysis in Nature Protocols yesterday: Mapping genome-wide transcription-factor binding sites using DAP-seq. The method is elegantly simple in its concept; PCR-free libraries from native gDNA are hybridised with affinity-tagged in vitro-expressed transcription factors, […]

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