18 10, 2018

Single-cell cancer sequencing on BioRxiv

By | October 18th, 2018|Categories: 10X Genomics, Methods and applications, Next-generation sequencing, Single-cell sequencing|0 Comments

Three recent papers from Sam Apraicio (@sajraparicio) and Sorab Shah (@SohrabShah) are well worth a read on BioRxiv. In June Kieran Cambell posted a paper describing computational methods to integrate single-cell DNA and RNA-Seq data. And in September Camila de Souza and Emma Laks posted reports […]

14 02, 2018

New products from @10XGenomics #AGBT18 workshop

By | February 14th, 2018|Categories: 10X Genomics, Conferences, Methods and applications, Next-generation sequencing|0 Comments

The 10XGenomics workshop just closed at AGBT and they announced some truly revolutionary new applications: single-cell feature barcoding, single-cell ATAC-Seq and single-cell CNV (feat CBGB). I’ll go through each of these in more detail below but I wanted to start by highlighting the success of single-cell analysis […]

28 03, 2017

HMW DNA extraction for long-reads on @nanopore or @10XGenomics

By | March 28th, 2017|Categories: 10X Genomics, Methods and applications, Next-generation sequencing|8 Comments

Long-reads require long DNA molecules which require high molecular weight (and undamaged) DNA. Extraction with your standard column is unlikely to be optimal. I’m starting to look at the best methods for HMW DNA extraction for long-read applications as my lab is supporting a couple of […]

22 03, 2017

10X Genomics 10x cheaper…and better too!

By | March 22nd, 2017|Categories: "Experimental design controls etc", 10X Genomics, Methods and applications, Next-generation sequencing, Single-cell sequencing, Uncategorized|1 Comment

Confession: this post may not actually make your 10X Genomics experiments ten times cheaper…but implement Demuxlet in your workflow and with the right sort of experiment you might just get there! Single-cell RNA-Seq might just have got a whole lot cheaper, thanks to a method […]

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 […]

14 09, 2016

10X Genomics publications

By | September 14th, 2016|Categories: 10X Genomics, Next-generation sequencing|0 Comments

Anyone that’s been reading Core-Genomics will have seen my interest in the technology from 10X Genomics. I’ve been watching and waiting for publications to come out to get a better understanding of how people are using the technology and thought you might like my current […]

9 09, 2016

10X Genomics phasing explained

By | September 9th, 2016|Categories: 10X Genomics, Next-generation sequencing|3 Comments

This post follows on from my previous one explaining the 10X Genomics single-cell mRNA-seq assay. This time round I’m really reviewing the method as described in a paper recently put up on the BioRxiv by 10X’s Deanna Church and David Jaffe: Direct determination of diploid genome […]

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 […]

12 02, 2016

AGBT16 10X Genomics workshop

By | February 12th, 2016|Categories: 10X Genomics, Single-cell sequencing|0 Comments

10X Genomics were one of the stars of the show at AGBT15, this year they’re bowling attendees over with new developments. They’ve obviously had an awfully busy year. They announced lots at JP Morgan (GenomeWeb, Core-Genomics). I got a sneak peak (as did Keith at […]

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