Explain Podcast

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 supportsresearch in genomics & transcriptomics by providing expertise andsequencing 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 1-8channels, each channel can be filled with multiple different samples- 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/⁠

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 supportsresearch in genomics & transcriptomics by providing expertise andsequencing 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

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 killed the stripey cat

Chapters:

00:00 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 supportsresearch in genomics & transcriptomics by providing expertise andsequencing 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 atHeinrich-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/⁠

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/