Explain Podcast – Details, episodes & analysis

Mixing up long and cheap

... soon we need to add "vs mid-reads"

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/⁠

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/⁠

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).

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/⁠

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:

00:00 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).

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/⁠

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).

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/⁠

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:

00:00 Intro

03:00 Fireflies

04:00 Energy

06:00 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 supportsresearch in genomics & transcriptomics by providing expertise andsequencing services. WGGC is a part of the Next Generation SequencingCompetence 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 ).

The Explain Podcast is recorded at the Medienlabor at the Heinrich-Heine University of Düsseldorf (https://medienlab.phil.hhu.de/). Our podcast is an outreach activity within the national genomicsfacility "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/

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

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/

The Explain Podcast hosts are Daniel Rickert (bioinformatician) and Iuliia Novoselova (physicist & communication trainer).

We aim to EXPLAIN key 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. We record without script: crisp energy awaits you!

Since 2018, West German Genome Center (WGGC) operates as the joint 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).

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/

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 nextgeneration 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 ofDüsseldorf 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/

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/⁠

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

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/⁠