Explain Podcast explain.pod

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

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).

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).

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).

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

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