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 […]

8 06, 2018

Single-cell indexing for methylation analysis (sci-MET)

By | June 8th, 2018|Categories: Library Prep, Methods and applications, Single-cell sequencing|0 Comments

Andrew Adey’s group at OHSU published sci-MET – a single cell method for whole-genome methylation analysis in Nature Biotech last month: Highly scalable generation of DNA methylation profiles in single cells. In this they described their indexing method and report on an analysis of over 3000 […]

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 […]

28 03, 2017

Single-cell analysis improved with consensus clustering

By | March 28th, 2017|Categories: Next-generation sequencing, Single-cell sequencing|0 Comments

Anyone interested in single-cell RNA-Seq analysis is likely to be interested in a paper published today by the Sanger in Nature Methods: Kiselev et al. (2017) SC3: consensus clustering of single-cell RNA-seq data. The new single-cell clustering tool performs better than 5 other methods: tSNE + k-means […]

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 […]

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: , |5 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 […]

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