sequencing

Improving ‘Noisy’ Long-read RNA-Seq

Chenchen Zhu from Stanford University presented at London Calling 2022 on the “Systematic assessment of long-read RNA-Seq datasets and its application in transcriptome analysis.” They are interested in understanding RNA isoforms using long-read sequencing. Differences in start sites and isoforms can lead to disease. The experimental workflow that Zhu shared was using reverse transcription and […]
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ONT-cappable-seq Enrichment of Primary Transcripts

Leena Putzeys from KU Leuven, Belgium spoke at London Calling 2022 about “Unlocking the transcriptomic architecture of bacterial viruses with ONT-cappable-seq.” Putzeys spoke about the use of phages as potential antibacterials and biotechnological applications. They noted that classic short-read RNA sequencing is difficult to interpret for phages. This is because short-read transcriptomes don’t distinguish between […]
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Fecal Samples for Epigenetic Age Estimations

Continuing with epigenetics, tonight I watched the London Calling 2022 session by Eveliina Hanski from the University of Oxford in the UK. The title of the session is “From laboratory to the wild: a non-invasive, MinION-based method for determining the epigenetic age of mice.” Hanski is a final year graduate student and is interested in […]
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The Epitranscriptome?

Eduardo Eyras from the Australian National University in Australia presented at London Calling 2022 a session entitled “RNA methylation detection at single-molecule resolution uncovers isoform-specific modifications during mouse brain development.” Eyras explained that chemical modifications of mRNA were discovered relatively recently and Boccaletto et al. 2021 noted >150 potential RNA modifications! However, only 6 have […]
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“Long POG”

Kieran O’Neill from Canada’s Michael Smith Genome Sciences Center (GSC), BC Cancer, Canada presented at London Calling 2022 on “Nanopore sequencing shows potential for personalised oncogenomics.” O’Neill spoke about the GSC’s work on genome research and sequencing. They have a Personalized Oncogenomics Program (POG) that consists of taking a biopsy, whole genome transcriptome analysis, reporting, […]
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Screening for Klinefelter Syndrome

Anne Kristine Schack from the University of Copenhagen and gMendel, Denmark spoke at London Calling 2022 about “A novel assay based on Oxford Nanopore technology for potential mass screening of Klinefelter syndrome.” They explained that Klinefelter Syndrome is a genetic disorder in which there is an additional X chromosome and it affects one in 500 […]
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Direct RNA Sequencing and Quantification with NanoCount

Josie Gleeson from the University of Melbourne, Australia presented at London Calling 2022 the ten-minute session entitled “Accurate expression quantification from nanopore direct RNA sequencing with NanoCount.” I am really interested in learning about transcriptomics with Nanopore devices and didn’t know about NanoCount. Gleeson spoke about how “long-read sequencing with Oxford Nanopore Technologies (ONT) can […]
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At Home Mitogenomes

“Affordable de novo generation of fish mitogenomes using amplification-free targeted enrichment and deep sequencing of long fragments” is the title of the London Calling 2022 session by Ana Ramon-Laca from NOAA Fisheries and the University of Washington that I watched tonight. They began by talking about eDNA surveys and metabarcoding tools to survey environments. Ramon-Laca […]
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Sequencing to Safeguard the Kākāpō

Continuing with London Calling 2022 recordings, tonight I watched Marissa Le Lec from the University of Otago in New Zealand and Lara Urban from Helmholtz Munich, Germany speak about “Portable real-time sequencing to safeguard critically endangered wildlife.” They spoke about mammalian predators including domestic cats affecting bird diversity. Le Lec spoke about the kākāpō, a […]
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