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Nanopore Digest: 15th November 2019

Fri 22nd November 2019

transcriptome sequencing

Welcome to the Oxford Nanopore digest - a regular newsletter of updates from the nanopore community.  You'll be able to find links to recent publications, presentations and other news.  If you'd like to get the digest in your inbox please let us know.

High throughput, error corrected nanopore single cell transcriptome sequencing

Short-read single-cell transcriptome sequencing is limited in its ability to understand cell-to-cell variability in splicing, fusion transcripts, and sequence diversity. In this pre-print, Lebrigand et al. demonstrate the application of long-read nanopore sequencing on the PromethION platform to analyse the transcriptome of >1,000 single cells isolated from murine brain. Cell barcodes were assigned with 99.8% accuracy to 67% of nanopore reads with identified poly-A sequences, and UMI assignment was 97.4% accurate for 76.4% of reads with an identified cell barcode. In total, they identified 18,439 GENCODE-annotated transcripts and 15,317 novel transcripts. The authors conclude that: “Single cell Nanopore sequencing with UMIs (ScNaUmi-seq) will facilitate high throughput single cell studies on RNA splicing, editing and imprinting and should also become a valuable tool for in depth studies of tumor heterogeneity”.

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London Calling 2020

Register to hear from a host of international speakers on topics including; structural variation, transcriptomics, assembly, methylation, targeted sequencing, metagenomics, and more

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