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.
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 - 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
Erschienen: 01.12.2023
Dauer: 00:38:39
Weitere Informationen zur Episode "Episode 5: Illumina Sequencing Part II"
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 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). CORRECTION: On the Illumina 1-channel chemistry, one base signal gets added, one removed at the enzymatic step: so that's one signal that stays, one that disappears, one that comes to shine and one that never shines. - DR
Erschienen: 13.11.2023
Dauer: 00:34:31
Weitere Informationen zur Episode "Episode 5: Illumina Sequencing Part I"
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 beginners: https://nij.ojp.gov/topics/articles/what-str-analysis MIT on genome assembly: https://www.youtube.com/watch?v=ZYW2AeDE6wU Fundamentals of genome assembly by Bioinformatics DotCa: https://www.youtube.com/watch?v=5wvGapmA5zM Genome assembly tips from F1000Research: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850084/ CD Genomics explaining some genome assembly metrics: https://www.cd-genomics.com/an-overview-of-genome-assembly.html Geneticeducation giving an intro to transcriptomics: https://geneticeducation.co.in/what-is-transcriptomics/ A slideshare explaining transcriptomics: https://www.slideshare.net/divyasrivastava17/transcriptome-analysis How to create a volcano plot in R: https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot-r/tutorial.html Bioinformatic walk-through by the galaxy project with a typical RNA-Seq experiment: https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-counts-to-genes/tutorial.html RNA splicing explained by arpan: https://www.youtube.com/watch?v=IJQv1H-2IoI khanacademy on RNA processing: https://www.khanacademy.org/science/ap-biology/gene-expression-and-regulation/transcription-and-rna-processing/a/eukaryotic-pre-mrna-processing 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).
Erschienen: 20.10.2023
Dauer: 01:07:17
Weitere Informationen zur Episode "Special Episode 2: How Sequencing is used"
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 - Slideshow giving an overview: https://www.slideshare.net/USDBioinformatics/ion-torrent-sequencing - biobinge explaining Iontorrent sequencing: https://biobinge.pubpub.org/pub/its/release/1 - rna-seqblog showing a comparison to Illumina: https://www.rna-seqblog.com/a-comparison-of-illumina-and-ion-torrent-sequencing-platforms-and-the-winner-is/ - Explainer by Shomu’s Biology: https://www.youtube.com/watch?v=0Ch5189aaCU 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).
Erschienen: 22.09.2023
Dauer: 00:52:32
Weitere Informationen zur Episode "Episode 4: Ion Torrent Sequencing"
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 sequencing: https://atdbio.com/nucleic-acids-book/Next-generation-sequencing#Sequencing-by-ligation-SOLiD - Biogene Blog on SOLiD sequencers: https://www.creative-biogene.com/blog/index.php/2017/02/22/the-next-generation-sequencing-platform-of-abi-company/ Chapters: 01:00 Intro 02:45 Ligation 06:50 Getting hairy balls 20:00 Bead 1 with DNA polonies 23:30 6 Base Jokers 24:00 2-Base encoding colours 29:15 Offsets and holes 35:00 Randomness and barcodes 37:25 Chemistry summary 40:30 Homopolymers are not the problem 46:30 SOLiDs fate 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).
Erschienen: 22.08.2023
Dauer: 00:51:54
Weitere Informationen zur Episode "Episode 3: SOLiD Sequencing"
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/ - Banana DNA extraction: https://askabiologist.asu.edu/activities/banana-dna BONUS: Directed, artifical evolution of enzymes: - Where it comes from: https://www.nobelprize.org/prizes/chemistry/2018/arnold/facts/ - Chemistryworld about the idea: https://www.chemistryworld.com/news/what-is-directed-evolution-and-why-did-it-win-the-chemistry-nobel-prize/3009584.article - A few of many results of this method: https://pdb101.rcsb.org/motm/228 - MIT News about adding robots to this: https://news.mit.edu/2021/robotic-directed-evolution-molecules-1230 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).
Erschienen: 04.08.2023
Dauer: 00:22:47
Weitere Informationen zur Episode "Special Episode 1: Kitchen Genomics - DIY DNA Isolation"
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 - Shomu's Biology on Pyrosequencing: https://www.youtube.com/watch?v=he6kJStE2zs - Quick Biochemistry Basics explaining the method: https://www.youtube.com/watch?v=wY8to-_zAEo - Bionity on Pyrosequencing: https://www.bionity.com/en/encyclopedia/454_Life_Sciences.html Chapters: 1:00 Intro 3:00 Fireflies 4:00 Energy 6:00 Luciferase Reaction 11:00 TTTTTTTTTTTTTTT...T? 14:00 microwell Plates 18:00 Pyrosequencing 25:00 Storage & Price 30:00 Teaser 31:00 Pyro? 34:00 Outro 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).
Erschienen: 14.07.2023
Dauer: 00:34:24
Weitere Informationen zur Episode "Episode 2: Pyrosequencing"
Iuliia is confused about RNA and Daniel doesn’t know the size of a DNA nucleotide Chapters: 00:00-Intro 02:00-DNA 08:27-Enzymes 13:05-RNAs, tRNAs 16:18-mRNAs, µRNAs, lncRNAs, circRNAs 21:35-Wobble 23:30-PCR 33:20-Sanger sequencing I 36:30-Gel electrophoresis 40:00-Sanger sequencing II 53:10-Teaser next Episode, Outro Topics: DNA, RNA, Protein, PCR, Gel Electrophoresis, Sanger Sequencing - The Royal Institution on the DNA Discovery: https://www.youtube.com/watch?v=_w2453iom9s - The discovery of DNA on science history: https://sciencehistory.org/education/scientific-biographies/james-watson-francis-crick-maurice-wilkins-and-rosalind-franklin/ - The New York Times on Franklins’ part: https://www.nytimes.com/2023/04/25/science/rosalind-franklin-dna.html - Wikipedias article on Proteins with history: https://en.wikipedia.org/wiki/Protein - Jrank on RNA: https://science.jrank.org/pages/5871/Ribonucleic-Acid-RNA-discovery-RNA.html - Microbe Notes showing the central dogma of molecular biology: https://microbenotes.com/central-dogma-replication-transcription-translation/ - ThoughtCo on RNA and DNA: https://www.thoughtco.com/dna-versus-rna-608191 - khanacademy explainers on PCR and Gel electrophoresis: https://www.khanacademy.org/science/ap-biology/gene-expression-and-regulation/biotechnology/a/polymerase-chain-reaction-pcr - Amoeba Sisters on PCR: https://www.youtube.com/watch?v=a5jmdh9AnS4 - Promega explaining Sanger sequencing: https://www.youtube.com/watch?v=dVRB4CaLizc - Microbe online’s writeup on Sanger sequencing: https://microbeonline.com/dna-sequencing-sanger-sequencing-method/ - LibreTextsBiology on Proteins and Enzymes: https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/03%3A_Biological_Macromolecules/3.07%3A_Proteins_-_Types_and_Functions_of_Proteins - excedr on Taq Polymerase and PCR: https://www.excedr.com/resources/taq-polymerase-what-is-it-and-what-does-it-do/ 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). P.S.: One DNA nucleotide is ~0.34 nanometers in „length“ - DR
Erschienen: 26.06.2023
Dauer: 00:53:49
Weitere Informationen zur Episode "Episode 1: Basics - from DNA to Sanger sequencing"
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).
Erschienen: 09.06.2023
Dauer: 00:05:29
