21 02, 2017

#AGBT17

By | February 21st, 2017|Categories: Conferences, Next-generation sequencing, Single-cell sequencing|0 Comments

This years #AGBT17 did not look as exciting as previous years have done, especially with all the major announcements being made at JP Morgan. In fact Illumina even went as far as to say they’d have no news at all during the conference! However there was […]

14 02, 2017

Understanding a 10XGenomics Cell ranger QC report

By | February 14th, 2017|Categories: "Experimental design controls etc", Single-cell sequencing|Tags: , |3 Comments

This post: “Understanding your 10XGenomics cell ranger report” originally appeared on my labs group blog but I thought that people working with single-cell who are at AGBT might like to read it too. Understanding your @10Xgenomics cell ranger reports The 10X Genomics Cell Ranger analysis […]

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 […]

1 02, 2017

Single-cell copy number analysis with SCI-Seq

By | February 1st, 2017|Categories: Next-generation sequencing, Single-cell sequencing|0 Comments

Andrew Adey’s group at the Department of Molecular & Medical Genetics in Oregon Health & Science University published SCI-seq in Nature Methods earlier this week (it has been on the BioRxiv since July). SCI-Seq is a method for single-cell copy number analysis that is likely […]

15 12, 2016

The 5 hardest things about single-cell sequencing

By | December 15th, 2016|Categories: Next-generation sequencing, Single-cell sequencing|2 Comments

Single-cell sequencing is making waves with many exciting developments over the last couple of years. Hardware is available from the companies like 10X Genomics, Fluidigm, Wafergen, BioRad (see GenomeWeb), RainDance (see GenomeWeb), Dolomite Bio. Chemistry for RNA and Genome sequencing such as SMART-Seq V4 and TruPrime, opens up all sorts […]

17 10, 2016

SIRVs: RNA-seq controls from @Lexogen

By | October 17th, 2016|Categories: Commissioned content, Next-generation sequencing, Single-cell sequencing|1 Comment

This article was commissioned by Lexogen GmbH. My lab has been performing RNA-seq for many years, and is currently building new services around single-cell RNA-seq. Fluidigm’s C1, academic efforts such as Drop-seq and inDrop, and commercial platforms from 10X Genomics, Dolomite Bio, Wafergen, Illumina/BioRad, RainDance and others makes establishing […]

16 09, 2016

Reporting on Fluidigm’s single-cell user meeting at the Sanger Institute

By | September 16th, 2016|Categories: Conferences, Next-generation sequencing, Single-cell sequencing|0 Comments

The Genomics community is pushing ahead fast on single-cell analysis methods as these are revolutionising how we approach biological questions. Unfortunately my registration went in too late for the meeting running at the Sanger Institute this week (Follow #SCG16 on Twitter), but the Fluidigm pre-meeting was a […]

28 07, 2016

10X Genomics single-cell 3’mRNA-seq explained

By | July 28th, 2016|Categories: 10X Genomics, Next-generation sequencing, Single-cell sequencing|2 Comments

10X Genomics have been very successful in developing their gel-bead droplet technology for phased genome sequencing and more recently, single-cell 3’mRNA-seq. I’ve posted about their technology before (at AGBT2016, and March and November 2015) and based most of what I’ve written on discussion with 10X […]

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