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.
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 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
Erschienen: 22.03.2024
Dauer: 01:10:38
Weitere Informationen zur Episode "Episode 9: Single Cell Sequencing"
Getting the most out of Machines Chapters: 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: 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).
Erschienen: 09.02.2024
Dauer: 01:10:43
Weitere Informationen zur Episode "Special Episode 3: PhiX / UMIs / QC"
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).
Erschienen: 16.01.2024
Dauer: 00:57:00
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).
Erschienen: 21.12.2023
Dauer: 00:56:27
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"
