Explain Podcast

explain.pod
  • 0.0 (0)
  • NATURAL SCIENCES
  • UPDATED MONTHLY

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. NEWS: 23andMe

    OCT 2

    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/

    22 min
  2. SE5: NGS in Immunology

    AUG 6

    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/⁠

    57 min
  3. E15: Singular Genomics | ATAC-seq

    MAY 28

    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/⁠

    46 min
  4. E14: Ultima Genomics + Element UltraQ

    APR 2

    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/⁠

    46 min
  5. E13: Sequencing by Avidity | Element Biosciences + XLEAP

    MAR 12

    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/⁠

    40 min
  6. E12: PacBio ONSO | Sequencing by binding

    JAN 28

    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/⁠

    55 min
  7. SE4: Long vs Short reads

    08/01/2024

    SE4: Long vs Short reads

    Mixing up long and cheap Chapters: 00:00:00 Intro 00:03:30 Florians history 00:13:50 Q&A Ressources for Bioinformatics 00:27:00 Long-read-tools.org 00:35:42 ONT || PacBio 00:57:00 Storage 01:09:00 Outro Up-to-date, raw prices:https://albertvilella.substack.com/p/march-2024-ngsspecs-update Dovetail comparing the two long-read technologies:https://dovetailbiopartners.com/2023/08/10/pacbio-vs-nanopore-unraveling-the-sequencing-odyssey-in-life-sciences/ Comparing PacBios old CLRs to ONT:https://academic.oup.com/g3journal/article/12/11/jkac192/6651842?login=true RNA Performance comparison, wonderful read:https://www.biorxiv.org/content/10.1101/2023.07.25.550582v1.full.pdf+html Integras 0.02$:https://www.integra-biosciences.com/united-states/en/blog/article/short-read-vs-long-read-sequencing 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 ). Our podcast is an outreach activity within the national genomics facility "West German Genome Center" funded by the DFG (https://www.dfg.de/) (No. 407493903) 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/⁠

    1h 12m
  8. E11: MGI DNA Nanoball sequencing

    07/02/2024

    E11: MGI DNA Nanoball sequencing

    Rolling in circles to make DNA yarns Chapters: 00:00 Bioinformatics Upper Crust Tools 04:04 STAR 05:00 MGI 15:00 Daniels first contact 20:00 Brief Market Overview 22:30 Short read market 26:00 DFG High Costs Sequencing Projects Application 29:20 QuickGen: Introns and Exons 35:00 Conclusion MGI vs Illumina: https://alitheagenomics.com/blog/how-do-rna-seq-results-compare-between-illumina-and-mgi-sequencing-platforms Rolling the circle: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568012/pdf/nihms894568.pdf MGI vs Illumina legal case:https://www.reuters.com/technology/illumina-ordered-pay-chinese-company-333-million-gene-sequencing-patent-case-2022-05-06/ The basics of MGIs technology: https://www.youtube.com/watch?v=gThcHHh4R0w DFG Application:https://www.dfg.de/de/aktuelles/neuigkeiten-themen/info-wissenschaft/2024/ifw-24-30 GTL/WGGC: https://www.gtl.hhu.de/wggc TSM link http://tsm.gtl.hhu.de/- submit your request and our colleagues will contact you 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 yourfeedback&questions via Email ( podcast[dot]explain[at]gmail[dot]com ). Our podcast is an outreach activity within the national genomics facility "West German Genome Center" funded by the DFG (https://www.dfg.de/) (No. 407493903) 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/⁠

    37 min
See All (22)

Trailer

About

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.

Information

  • Creator
    explain.pod
  • Years Active
    2023 - 2025
  • Episodes
    22
  • Rating
    Clean
  • Copyright
    © explain.pod
  • Show Website
    Explain Podcast