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PODCAST

Explain Podcast

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.

science natural sciences

All Episodes

00:21:59

NEWS: 23andMe

Explain Podcast ·

2025/10/02

This time something

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00:57:00

SE5: NGS in Immunology

Explain Podcast ·

2025/08/06

The science of white blood cells, and much moreChapters:05:30 Immunology how?22:05 22q11.2 deletion syndrome34:30 Scientific collaboration40:00 Data losses50:00 Flip it!53:00 outlook 2030Links:mini-immunology intro:https://www.youtube.com/watch?v=k9QAyP3bYmc22Q e. V. - zentraler Anlaufpunkt für Menschen mit Deletionssyndrom 22q11 oder Duplikationssyndrom 22q11 im deutschsprachigen Raum https://www.wirsind22q.de/aus-dem-verein/vorstandPodcast for young immunologists from young immunologists

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00:46:07

E15: Singular Genomics | ATAC-seq

Explain Podcast ·

2025/05/28

Sharing a flowcell, reinventedChapters:- 00:00 usegalaxy.org- 07:55 Singular Genomics start- 21:55 Max Reads- 29:40 DNA Structure / ATAC-seqSetup 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/d41586-023-00512-4How max reads

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00:46:20

Episode 14: Ultima Genomics + Element UltraQ

Explain Podcast ·

2025/04/02

Spinnin' bases on wafers to do mostly natural SBSChapters:- 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 ncRNAUltimas homepage: https://www.ultimagenomics.com/Nature paper with the chemistry: https://www.nature.com/articles/s41587-022-01452-6Elements UltraQ

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00:39:42

Episode 13: Sequencing by Avidity (Element...

Explain Podcast ·

2025/03/12

Because sometimes a jellyfish prevents quenchingChapters:01:00 - XLeap update from Illumina08:00 - Avidites start, splitting the problems13:20 - In-depth comparison to Illumina22:00 - Element summary23:30 - Bioinformatics tools: Jellyfish, KAT25:00 - QuickGen: GWASIllumina about their XLeap: https://www.illumina.com/science/genomics-research/articles/data-quality-q-scores.htmlSandiegomics about element: https://sandiegomics.com/element-beats-illumina-to-the-200-genome/Nature paper about the

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00:54:37

Episode 12: Sequencing by binding (PacBio ONSO)

Explain Podcast ·

2025/01/28

Because only one type of nucleotide is not complicated enoughChapters: 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:

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01:11:56

Special Episode 4: Long vs Short reads

Explain Podcast ·

2024/08/01

Mixing up long and cheapChapters: 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

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00:36:54

Episode 11: MGI DNA Nanoball sequencing

Explain Podcast ·

2024/07/02

Rolling in circles to make DNA yarnsChapters: 00:01 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:

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00:48:12

Episode 10: Genome Mapping

Explain Podcast ·

2024/05/27

Who needs all bases anyway?Chapters: 03:00 Phasing 08:50 Not Sequencing, really 14:00 Bionano Saphyr Chip 26:00 Nabsys - going electric 29:30 Tools available 39:00 QuickGen with Iuliia: Transposons! Links: Small explainer by CAP: https://www.cap.org/member-resources/articles/optical-genome-mapping-a-tool-with-significant-potential-from-discovery-to-diagnostics What genome mapping can be used for: https://www.mdpi.com/2073-4425/12/3/398 Finding SVs with genome mapping:

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01:10:38

Episode 9: Single Cell Sequencing

Explain Podcast ·

2024/03/22

Chapters:08:00 Gambling 15:00 Bubbles 30:00 Holes 57:30 One more thing 1:07:00 Finale 1:08:00 Finale of season 1! Eric Chow explaining single cell sequencing: https://www.youtube.com/watch?v=k9VFNLLQP8c Overview of things to consider: https://www.youtube.com/watch?v=VWUPKrnRvoQ How to analyze single cell data: https://www.youtube.com/watch?v=5HBzgsz8qyk A very good single cell analysis toolkit: https://satijalab.org/seurat/ Explainer for the rough

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01:10:43

Special Episode 3: PhiX / UMIs / QC

Explain Podcast ·

2024/02/09

Getting the most out of MachinesChapters: 04:30 PhiX 14:30 low complexity 19:30 UMIs 32:10 FastQC 43:00 MultiQC 56:40 PycoQC PhiX concentrations for loading a validation run: https://knowledge.illumina.com/instrumentation/general/instrumentation-general-reference_material-list/000001536 Dnatech on why UMIs are used: https://dnatech.genomecenter.ucdavis.edu/faqs/what-are-umis-and-why-are-they-used-in-high-throughput-sequencing/ BMH learning on UMIs:

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00:57:00

Episode 8: Nanopore

Explain Podcast ·

2024/01/16

Pushing spaghetti through holes Chapers: 00:00 Intro 11:15 Measuring Ions 17:00 Quality 23:00 Duplex 24:30 MinION 25:15 PromethION 28:20 Methylation 29:00 Direct RNA sequencing 38:25 Basecalling 46:00 Basecalling bias 53:50 Sequencing proteins - Nanopore explainer: https://nanoporetech.com/applications/dna-nanopore-sequencing - Oxsci explaining the technology: https://oxsci.org/pore-over-this-advances-in-dna-sequencing/ - History of

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00:56:27

Episode 7: PacBio

Explain Podcast ·

2023/12/21

Zipping rounds in zeptoliters Chapters: 00:00 Intro 07:00 Laser 09:00 Zeptoliters 13:30 Polymerase speed 19:00 Error rate 22:00 SMRT Cell 25:45 ccs 30:00 Fragment size 34:30 Megaruptor 38:20 Data flow 47:00 SVs 53:00 MAS Seq - Starter: https://www.nature.com/articles/s41366-021-00824-3 - Karobben on PacBio sequencing: https://karobben.github.io/2023/10/30/Bioinfor/PacBio/ - bioinformticamente explaining the technology: https://bioinformaticamente.com/2020/12/05/pacbio-sequencing/ - Basic

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00:38:39

Episode 6: Illumina Sequencing Part II

Explain Podcast ·

2023/12/01

Glued DNA bridges and rainbow clusters Chapters: 00:43-Flowcells 03:40-DNA glued to glass 09:00-Bridge amplification 15:50-Cluster density and patterned Flowcells 28:30-Illumina SBS summary 30:30-Limits 33:00-Multiplexing and Demultiplexing - enseqlopedia on patterned vs unpatterned flowcell: http://enseqlopedia.com/2016/01/almost-everything-you-wanted-to-know-about-illumina-hiseq-4000-and-some-stuff-you-didnt/ - ClevaLabs on Illumina sequencing: https://www.youtube.com/watch?v=WKAUtJQ69n8 -

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00:34:31

Episode 5: Illumina Sequencing Part I

Explain Podcast ·

2023/11/13

Colour mixing in PHRED space Chapters: 00:00 Nucleotides level 2 09:00 Cycles 12:00 Not-so-wobbly mutations 15:30 Reducing colourspace 22:30 Cutting connections 28:14 Costs and PHRED - ClevaLabs on Illumina sequencing: https://www.youtube.com/watch?v=WKAUtJQ69n8 - Yourgenome on how the Illumina workflow works: https://www.yourgenome.org/facts/what-is-the-illumina-method-of-dna-sequencing/ - DNATech comparing Illumina

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01:07:17

Special Episode 2: How Sequencing is used

Explain Podcast ·

2023/10/20

Iuliia killed the stripey cat Chapters: 00:01:00 Intro 00:04:44 Stripes 00:11:40 Sanger with colors 00:17:20 CATCATCAT... 00:33:20 Planes 00:38:15 Genome assembly 00:40:00 Transcriptomics 01:01:00 Hi-C Why women are stripey: https://www.youtube.com/watch?v=BD6h-wDj7bw Future-science about str profiling: https://www.future-science.com/doi/10.2144/000112582 Mark Santucci explaining str profiles: https://www.youtube.com/watch?v=Eg3gH2wmAW8 NIJ explaining the theory for

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00:52:32

Episode 4: Ion Torrent Sequencing

Explain Podcast ·

2023/09/22

H+ ions and where we can find them Chapters: 00:00 Intro 04:26 pH 08:04 DNA Polymerase reaction with H+ 12:30 Nucleotides 16:30 Homopolymer problem, but different 19:30 PCR is mean to some bases 24:30 AmpliSeq 33:40 Today’s status 38:58 cfDNA 40:00 PHRED vs Qscore 44:59 Chip scaling and prices 51:00 Outro - bitesizedbio on the technology: https://bitesizebio.com/27399/all-in-the-chip-ion-torrent-sequencers/ - Quick explainer from Basic Biochem: https://www.youtube.com/watch?v=vMUnN2Y48Us -

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00:51:54

Episode 3: SOLiD Sequencing

Explain Podcast ·

2023/08/22

If ligation is more your thing - Special Operations explaining SOLiD Sequencing: https://www.youtube.com/watch?v=YLT-DUeaLms - Writeup by the Apollo Institute on SOLiD Sequencing: https://apollo-institute.org/solid-sequencing/ - Quick run-through video by ABI: https://www.youtube.com/watch?v=nlvyF8bFDwM - Ars technica about the technology: https://arstechnica.com/science/2009/12/dna-sequencing-gets-solid-with-built-in-error-detection/ - atdbio explaining SOLiD

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00:22:47

Special Episode 1: Kitchen Genomics - DIY DNA Isolation

Explain Podcast ·

2023/08/04

Iuliia and Daniel have fun with salt water and alcohol Chapters: 00:00:00 DIY DNA isolation 00:15:38 Directed evolution of Enzymes DNA isolation in your kitchen - Experiment during the episode: https://www.instructables.com/How-to-Extract-Your-Own-DNA-Using-Household-Kitche/ - Another protocol with the same approach: https://learning-center.homesciencetools.com/article/how-to-extract-dna-at-home/ - Extract DNA from a strawberry: https://www.popsci.com/diy/diy-science-project-strawberrry-dna/ -

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00:34:24

Episode 2: Pyrosequencing

Explain Podcast ·

2023/07/14

Daniel and Iuliia are confused about fireflies - Scientific american on how fireflies create light: https://www.scientificamerican.com/article/how-and-why-do-fireflies/ - A small breakdown of a typical Pyrosequencing workflow: https://www.news-medical.net/life-sciences/What-is-Pyrosequencing.aspx - Biology-pages on Pyrosequencing: https://www.biology-pages.info/P/Pyrosequencing.html - Biotechfront on Pyrosequencing: https://www.biotechfront.com/2021/04/pyrosequencing-principle-and-steps.html -

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22 results

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