Explain Podcast

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The Podcast Explain is for everyone interested in DNA/RNA sequencing or technology in general. As Iuliia doesn't have a solid background in sequencing, she keeps asking "simple" - even silly at times - questions and Daniel gives his best to make us understand.

  1. Array Sequencing

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    Array Sequencing

    For when matching and sticking is enough to get Since 2018, the West German Genome Center (⁠https://wggc.de/⁠) supports research in genomics & transcriptomics by providing expertise and sequencing services. WGGC is a part of the Next Generation Sequencing Competence Network (NGS-CN: ⁠https://ngs-kn.de/⁠) – network of NGS core facilities in Germany. Listen to our podcast and we're happy to receive your feedback&questions via Email (podcast[dot]explain[at]gmail[dot]com ). License Notice This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made. Attribution: Podcast Title: Explain Podcast Creators: Iuliia Novoselova, Daniel Rickert Website: ⁠⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

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  2. Sequencing by Expansion (SBX)

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    Sequencing by Expansion (SBX)

    After 454 now the second try by Roche: Axelios. Preprint: https://www.biorxiv.org/content/10.1101/2025.02.19.639056v1 Read here about the PoC: https://www.pnas.org/doi/full/10.1073/pnas.1601782113 Current state (2025): https://www.nejm.org/doi/full/10.1056/NEJMc2512825 Correction: the 5B flow cell will arrive for the NovaseqX(+), not for the Nextseq2000 Also: PacBio makes sequencing cheaper: https://www.pacb.com/press_releases/pacbio-announces-major-advances-for-revio-and-vega-to-lower-genome-cost-and-expand-multiomic-capabilities/⁠ Roche about SBX: https://sequencing.roche.com/global/en/article-listing/sequencing-platform-technologies.html Roche from a conference: https://www.youtube.com/watch?v=YN2meswiCiQ Since 2018, West German Genome Center (⁠https://wggc.de/⁠) operates as the next generation sequencing facility and supports research in genomics & transcriptomics by providing expertise and sequencing services. WGGC is a part of the Next Generation Sequencing Competence Network (NGS-CN: ⁠https://ngs-kn.de/⁠) – network of NGS core facilities in Germany. Listen to our podcast and we're happy to receive your feedback&questions via Email (podcast[dot]explain[at]gmail[dot]com ). License Notice This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made. Attribution: Podcast Title: Explain Podcast Creators: Iuliia Novoselova, Daniel Rickert Website: ⁠⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

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  3. NEWS: 23andMe

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    NEWS: 23andMe

    This time something different. Sources: https://www.23andme.com/privacy/ https://verbraucherschutzforum.berlin/2025-03-25/23andme-meldet-insolvenz-an-was-nutzer-jetzt-wissen-sollten-357738/ https://en.wikipedia.org/wiki/23andMe_data_leak https://www.cshub.com/attacks/news/23andme-hacker-leaks-data https://www.cbsnews.com/news/dna-privacy-at-home-tests-23andme-ancestrydna-sell-data-to-third-parties/ https://techcrunch.com/2025/03/24/23andme-faces-an-uncertain-future-so-does-your-genetic-data/ https://www.theverge.com/2024/9/13/24243986/23andme-settlement-dna-data-breach-lawsuit https://newsroom.regeneron.com/news-releases/news-release-details/regeneron-enters-asset-purchase-agreement-acquire-23andmer-256/

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  4. SE5: NGS in Immunology

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    SE5: NGS in Immunology

    The science of white blood cells, and much more Chapters: 05:30 Immunology how? 22:05 22q11.2 deletion syndrome 34:30 Scientific collaboration 40:00 Data losses 50:00 Flip it! 53:00 outlook 2030 Links: mini-immunology intro: https://www.youtube.com/watch?v=k9QAyP3bYmc 22Q e. V. - zentraler Anlaufpunkt für Menschen mit Deletionssyndrom 22q11 oder Duplikationssyndrom 22q11 im deutschsprachigen Raum https://www.wirsind22q.de/aus-dem-verein/vorstand Podcast for young immunologists from young immunologists https://theyoungimmunologist.buzzsprout.com/ Contact Nora here https://www.linkedin.com/in/nora-balzer-phd-253a767b Some information about training courses and events https://www.immunology.org/traininghttps://dgfi.org/dgfi-en/academy-of-immunology/ Since 2018, West German Genome Center (⁠https://wggc.de/⁠) operates as the next generation sequencing facility and supports research in genomics & transcriptomics by providing expertise and sequencing services. WGGC is a part of the Next Generation Sequencing Competence Network (NGS-CN: ⁠https://ngs-kn.de/⁠) – network of NGS core facilities in Germany. Listen to our podcast and we're happy to receive your feedback&questions via Email (podcast[dot]explain[at]gmail[dot]com ). License Notice This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made. Attribution: Podcast Title: Explain Podcast Creators: Iuliia Novoselova, Daniel Rickert Website: ⁠⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

    ٥٧ من الدقائق
  5. E15: Singular Genomics | ATAC-seq

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    E15: Singular Genomics | ATAC-seq

    Sharing a flowcell, reinvented Chapters: - 00:00 usegalaxy.org - 07:55 Singular Genomics start - 21:55 Max Reads - 29:40 DNA Structure / ATAC-seq Setup galaxy on local hardware: https://galaxyproject.org/admin/get-galaxy/ G4 is competing with Illumina: https://www.genengnews.com/topics/omics/fast-and-flexible-singulars-g4-takes-aim-at-illuminas-sequencing-superiority/ Singulars chemistry is one of many: https://www.nature.com/articles/d41586-023-00512-4 How max reads works: https://techwriting.singulargenomics.com/max-read/Max-Read-Kit-User-Guide-600026.pdf Small intro to DNA Structures: https://en.wikipedia.org/wiki/Nucleic_acid_quaternary_structure Intro to ATAC-seq: https://www.nature.com/articles/s41596-022-00692-9 PS: As of 2025, Singular does not advertise DNA/RNA Sequencing on their G4 anymore, but shifted to spatial data, including their G4X: https://www.singulargenomics.com/ Since 2018, West German Genome Center (⁠https://wggc.de/⁠) operates as the next generation sequencing facility and supports research in genomics & transcriptomics by providing expertise and sequencing services. WGGC is a part of the Next Generation Sequencing Competence Network (NGS-CN: ⁠https://ngs-kn.de/⁠) – network of NGS core facilities in Germany. Listen to our podcast and we're happy to receive your feedback&questions via Email (podcast[dot]explain[at]gmail[dot]com ). License Notice This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made. Attribution: Podcast Title: Explain Podcast Creators: Iuliia Novoselova, Daniel Rickert Website: ⁠⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

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  6. E14: Ultima Genomics + Element UltraQ

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    E14: Ultima Genomics + Element UltraQ

    Spinnin' bases on wafers to do mostly natural SBS Chapters: - 00:00 Ultima ePCR with beads - 07:10 Spinning the wafer, nucleotides, no blocking - 14:30 Ultima ppmSeq + Element UltraQ - 25:30 How Element UltraQ was born - 30:30 snakemake, cromwell, nextflow - 36:50 ncRNA Ultimas homepage: https://www.ultimagenomics.com/ Nature paper with the chemistry: https://www.nature.com/articles/s41587-022-01452-6 Elements UltraQ chemistry: https://www.elementbiosciences.com/cloudbreak-ultraq-enhanced-sequencing-accuracy-when-precision-matters-most Snakemake: https://snakemake.readthedocs.io/en/stable/ Nextflow: https://www.nextflow.io/docs/latest/index.html Cromwell: https://cromwell.readthedocs.io/en/stable/ Small overview of not all ncRNA types: https://microbenotes.com/types-of-rna/ Since 2018, West German Genome Center (https://wggc.de/) operates as the next generation sequencing facility and supports research in genomics & transcriptomics by providing expertise and sequencing services. WGGC is a part of the Next Generation Sequencing Competence Network (NGS-CN: https://ngs-kn.de/) – network of NGS core facilities in Germany. Listen to our podcast and we're happy to receive your feedback&questions via Email (podcast[dot]explain[at]gmail[dot]com ). License Notice This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made. Attribution: Podcast Title: Explain Podcast Creators: Iuliia Novoselova, Daniel Rickert Website: ⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

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  7. E13: Sequencing by Avidity | Element Biosciences + XLEAP

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    E13: Sequencing by Avidity | Element Biosciences + XLEAP

    Because sometimes a jellyfish prevents quenching Chapters: 01:00 - XLeap update from Illumina 08:00 - Avidites start, splitting the problems 13:20 - In-depth comparison to Illumina 22:00 - Element summary 23:30 - Bioinformatics tools: Jellyfish, KAT 25:00 - QuickGen: GWAS Illumina about their XLeap: https://www.illumina.com/science/genomics-research/articles/data-quality-q-scores.html Sandiegomics about element: https://sandiegomics.com/element-beats-illumina-to-the-200-genome/ Nature paper about the chemistry: https://www.nature.com/articles/s41587-023-01750-7 Jellyfish for k-mer counting: https://github.com/gmarcais/Jellyfish GWAS Catalog: very nice data collection: https://www.ebi.ac.uk/gwas/diagram Correcting population-based GWAS bias: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1011242 Since 2018, West German Genome Center (https://wggc.de/) operates as the next generation sequencing facility and supports research in genomics & transcriptomics by providing expertise and sequencing services. WGGC is a part of the Next Generation Sequencing Competence Network (NGS-CN: https://ngs-kn.de/) - network of NGS core facilities in Germany. Listen to our podcast and we're happy to receive your feedback&questions via Email (podcast[dot]explain[at]gmail[dot]com ). License Notice This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made. Attribution: Podcast Title: Explain Podcast Creators: Iuliia Novoselova, Daniel Rickert Website: ⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

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  8. E12: PacBio ONSO | Sequencing by binding

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    E12: PacBio ONSO | Sequencing by binding

    Because only one type of nucleotide is not complicated enough Chapters: 01:35 Introducing old problems 15:30 More Phred, more better 34:40 QuickGen: genetic testing 47:40 Bioinformatics tools: samtools PacBio ONSO Specs: https://www.pacb.com/wp-content/uploads/Onso-specification-sheet.pdf SBB explained by PacBio: https://www.pacb.com/blog/sbb-sequencing/ Why higher quality is better: https://pmc.ncbi.nlm.nih.gov/articles/PMC11331594/ Short read sequencing market heating up: https://www.nature.com/articles/s41587-022-01632-4 SBB for visual learners: https://www.youtube.com/watch?v=i_mSaNBOVmQ Since 2018, West German Genome Center (https://wggc.de/)operates as the next generation sequencing facility and supports research in genomics & transcriptomics by providing expertise and sequencing services. WGGC is a part of the Next Generation Sequencing Competence Network (NGS-CN: https://ngs-kn.de/) - network of NGS core facilities in Germany. Listen to our podcast and we're happy to receive your feedback&questions via Email (podcast[dot]explain[at]gmail[dot]com ). License Notice This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made. Attribution: Podcast Title: Explain Podcast Creators: Iuliia Novoselova, Daniel Rickert Website: ⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

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The Podcast Explain is for everyone interested in DNA/RNA sequencing or technology in general. As Iuliia doesn't have a solid background in sequencing, she keeps asking "simple" - even silly at times - questions and Daniel gives his best to make us understand.

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