Explain Podcast

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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.

AUG 1

Special Episode 4: 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)

1h 12m
JUL 2

Episode 11: 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 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)

37 min
MAY 27

Episode 10: Genome Mapping

Who needs all bases anyway? Chapters: 00:00 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: https://www.nature.com/articles/s41408-024-01059-x Bionano github repos: https://github.com/search?q=bionano&type=repositories&s=updated&o=desc Listen to our podcast and send your feedback to podcast[dot]explain[at]gmail[dot]com Since 2019, 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-cn.de/ – network of NGS core facilities in Germany. The Explain Podcast is recorded at the Multimediazentrum at Heinrich-Heine University of Düsseldorf https://www.mmz.hhu.de/ Our podcast is an outreach activity within the national genomics facility ”West German Genome Center” funded by the Ministerium für Kultur und Wissenschaft des Landes Nordrhein-Westfalen https://www.mkw.nrw/land-foerdert-spitzenzentrum-fuer-genomsequenzierung-nordrhein-westfalen/

48 min
MAR 22

Episode 9: Single Cell Sequencing

Chapters: 00:00 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 workflow: https://www.technologynetworks.com/genomics/articles/understanding-single-cell-sequencing-how-it-works-and-its-applications-357578 Quick explainer on single cell sequencing: https://www.the-scientist.com/single-cell-sequencing-in-a-nutshell-71048 A method-overview paper: https://www.nature.com/articles/s12276-020-00499-2 Comparing BD Parse and 10xGenomics: https://pubmed.ncbi.nlm.nih.gov/33414681/ Pseudotime analysis: https://bioconductor.org/books/3.14/OSCA.advanced/trajectory-analysis.html 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 send your feedback to ( podcast[dot]explain[at]gmail[dot]com ). The Explain Podcast is recorded at the Medienlabor at Heinrich-Heine University of Düsseldorf (https://medienlab.phil.hhu.de/). 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). PS: I do not know how in the Parse approach the cells are treated to let the ligase and DNA enter each cell, but do not let RNA flow out of the cell at the same time. -DR

1h 11m
FEB 9

Special Episode 3: PhiX / UMIs / QC

Getting the most out of Machines Chapters: 00:00 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: https://www.youtube.com/watch?v=sRPMsnhIBK0 FastQC for QC of .fastq(.gz) files: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ A FastQC report from a „good“ sample: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/good_sequence_short_fastqc.html multiqc for summarizing QC reports: https://multiqc.info/ UMI-tools for working with UMI data: https://umi-tools.readthedocs.io/en/latest/ pycoQC for Nanopore QC: https://github.com/a-slide/pycoQC 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 ). The Explain Podcast is recorded at the Medienlabor at Heinrich-Heine University of Düsseldorf (https://medienlab.phil.hhu.de/). 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).

1h 11m
JAN 16

Episode 8: Nanopore

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 Nanopore: https://www.whatisbiotechnology.org/index.php/science/summary/nanopore/nanopore-sequencing-makes-it-possible-to-decode-the - Shmou’s Biology explaining Nanopore sequencing: https://www.youtube.com/watch?v=MlluAjhzXqI - A direct comparison of Nanopore and Illumina output: https://medresearch.umich.edu/office-research/about-office-research/biomedical-research-core-facilities/advanced-genomics-core/technologies/next-generation-sequencing - A nice Nanopore QC tool we use: https://hpc.nih.gov/apps/pycoQC.html - How a MinION looks like: https://www.whatech.com/og/markets-research/medical/658327-global-nanopore-sequencing-market-2020 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 ). The Explain Podcast is recorded at the Medienlabor at Heinrich-Heine University of Düsseldorf (https://medienlab.phil.hhu.de/). 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).

57 min
12/21/2023

Episode 7: PacBio

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 Biochem explainer of SMRT sequencing: https://www.youtube.com/watch?v=H2gUmRf-K1c - Genomics Lab explaining it: https://www.youtube.com/watch?v=vRhUSjhygDU - PacBio explaining BAM Tags: https://pacbiofileformats.readthedocs.io/en/13.0/BAM.html - Megaruptor3 explainer (how we make the right sized fragments) : https://www.youtube.com/watch?v=zVhqnkQL8zo - How we select the right sized fragments: https://www.youtube.com/watch?v=A25C8xfBbq8 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 ). The Explain Podcast is recorded at the Medienlabor at Heinrich-Heine University of Düsseldorf (https://medienlab.phil.hhu.de/). 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).

56 min
12/01/2023

Episode 6: Illumina Sequencing Part II

Glued DNA bridges and rainbow clusters Chapters: 00:00-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 - Yourgenome on how the Illumina workflow works: https://www.yourgenome.org/facts/what-is-the-illumina-method-of-dna-sequencing/ - DNATech comparing Illumina Machines: https://dnatech.genomecenter.ucdavis.edu/illumina-high-throughput-sequencing/ - iBiology on sample preparation for Illumina sequencing: https://www.youtube.com/watch?v=PFwSe09dJX0 - StatQuest on how to use Illumina sequencing for RNA analysis: https://www.youtube.com/watch?v=tlf6wYJrwKY - Illumina Flowcell and sequencing machines pictures: https://www.illumina.com/company/news-center/multimedia-images.html - Nice explainer about paired-end sequencing: https://www.youtube.com/watch?v=gVrmfLXJRGM 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 send your feedback to ( podcast[dot]explain[at]gmail[dot]com ). The Explain Podcast is recorded at the Medienlabor at Heinrich-Heine University of Düsseldorf (https://medienlab.phil.hhu.de/). 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). Clarification: Each Flowcell on the Illumina platform has 1-8 channels, each channel can be filled with multiple different samples - DR

39 min

TRAILER

Teaser

The Explain Podcast hosts are bioinformatician Daniel and scientific coordinator Iuliia. We aim to EXPLAIN key next generation sequencing techniques and how these techniques contribute to our everyday life.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. Since 2018, West German Genome Center (WGGC) 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) - 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 ). The Explain Podcast is recorded at the Medienlabor at Heinrich-Heine University of Düsseldorf. Our podcast is an outreach activity within the national genomics facility "West German Genome Center" funded by DFG (No. 407493903).

06/09/2023

•

5 min

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.

Creator

explain.pod
Years Active

2023 - 2024
Episodes

16
Rating

Clean
Copyright

© explain.pod
Show Website

Explain Podcast