Year: 2023

Combined Transcriptome and Epitranscriptome in the Human Brain

Josie Gleeson from The University of Melbourne in Australia presented at London Calling 2023 about “Integrating the transcriptome and epitranscriptome of the human brain using direct RNA sequencing.” They spoke about the advantages of direct RNA sequencing with Oxford Nanopore Technologies: you obtain splicing patterns, isoform quantification, polyA tail length, modified nucleotides, and novel exon/intron […]
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EpiGLowS for Genotyping

Oscar Gonzalez-Recio from the National Institute for Agricultural and Food Research and Technology at the Spanish National Research Council in Spain presented at London Calling 2023 on “(Epi)genotyping by low-pass sequencing using nanopore technologies.” Gonzalez-Recio noted that this worm has been accepted for publication. They started with a history of modern genomic breeding and how […]
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m6A and Epitranscriptomics

Jade Forster from the University of Southampton in the UK presented at London Calling 2023 about “Identifying m6A RNA modifications in neuroblastoma cell lines using nanopore sequencing.” This session was timely as we are doing our first direct RNA sequencing experiment and GridION run! Forster spoke about epitranscriptomics and RNA modifications. They noted that the […]
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Improving Phasing Methods

What a busy day! We tried VolTRAX and Miro library preps today as part of the PORES workshop. We also did DNA extractions, a Miroculus workshop, and lots of moving around. Tonight I watched the London Calling 2023 session entitled “MethPhaser: automated methylation-based haplotype phasing of human genomes with Oxford Nanopore sequencing” with Fritz Sedlazeck […]
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Genome-wide Methylation Evaluation for Genetic Diagnosis

Miranda Galey from the University of Washington spoke at London Calling 2023 about “MeOW: genome-wide identification of differentially methylated regions using Oxford Nanopore long-read sequencing data.” Galey explained how long-read sequencing can shorten the time to diagnosis. The noted that methylated nucleotides have different current patterns that can be detected. The advantage of long-read sequencing […]
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Heterogeneity in Methylation Patterns

Tonight I watched the London Calling 2023 session entitled “Genome-wide single-molecule analysis of DNA methylation by nanopore sequencing reveals heterogeneous patterns” presented by Lyndsay Kerr from the University of Edinburgh in the UK. They spoke about the novel way of analyzing methylation patterns from single-molecule reads. Kerr explained that DNA methylation is a “repressive epigenetic […]
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Single-cell Mutation Profiling and Engineering

“A single-cell approach to cancer mutation discovery and CRISPR phenotypic modeling” was the title of the London Calling 2023 session by Hanlee Ji from Stanford University. Ji spoke about the use of single cell genomics and variant analysis. They spoke about how cancer mutations and clonal variation can be detected. In addition, CRISPR technologies allow […]
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Nanopore Sequencing for Equitable One Health

Lara Urban from the Helmholtz AI Institute, Helmholtz Pioneer Campus, & the Technical University of Munich in Germany spoke at London Calling 2023 about “Real-time genomics for One Health.” They explained that the concept of One Health is that the health of everything on our planet is interrelated. Urban explained how nanopore sequencing can unlock […]
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Sharing Insights about Rare Disease Research with ONT

Tonight I watched a London Calling 2023 session that was the rare disease research panel Q&A. One question was about the importance of methylation in rare diseases. Panelists were speakers from other London Calling 2023 sessions. They noted that sample type is important, as tissue and peripheral blood may be very different in terms of […]
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Direct RNA Sequencing with RNA004

We have been trying bacterial transcriptomics using Nanopore sequencing. I am particularly interested in direct RNA sequencing. Tonight I watched the London Calling 2023 session by Libby Snell, Principal Scientists/Applications at Oxford Nanopore Technologies, and Martin Smith from Sainte-Justine University Hospital Research Center in Canada. They presented a session entitled “Direct RNA sequencing update (SQK-RNA004): […]
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