Episodios
-
Spinnin' bases on wafers to do mostly natural SBS
Chapters:
- 00:00 Ultima ePCR with beads
- 07:10 Spinning the wafer, nucleotides, no blocking
- 14:30 Ultima ppmSeq + Element UltraQ
- 25:30 How Element UltraQ was born
- 30:30 snakemake, cromwell, nextflow
- 36:50 ncRNA
Ultimas homepage: https://www.ultimagenomics.com/
Nature paper with the chemistry: https://www.nature.com/articles/s41587-022-01452-6
Elements UltraQ chemistry:
https://www.elementbiosciences.com/cloudbreak-ultraq-enhanced-sequencing-accuracy-when-precision-matters-most
Snakemake: https://snakemake.readthedocs.io/en/stable/
Nextflow: https://www.nextflow.io/docs/latest/index.html
Cromwell: https://cromwell.readthedocs.io/en/stable/
Small overview of not all ncRNA types: https://microbenotes.com/types-of-rna/
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 ).
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/
-
Because sometimes a jellyfish prevents quenching
Chapters:
01:00 - XLeap update from Illumina
08:00 - Avidites start, splitting the problems
13:20 - In-depth comparison to Illumina
22:00 - Element summary
23:30 - Bioinformatics tools: Jellyfish, KAT
25:00 - QuickGen: GWAS
Illumina about their XLeap: https://www.illumina.com/science/genomics-research/articles/data-quality-q-scores.html
Sandiegomics about element: https://sandiegomics.com/element-beats-illumina-to-the-200-genome/
Nature paper about the chemistry: https://www.nature.com/articles/s41587-023-01750-7
Jellyfish for k-mer counting: https://github.com/gmarcais/Jellyfish
GWAS Catalog: very nice data collection: https://www.ebi.ac.uk/gwas/diagram
Correcting population-based GWAS bias: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1011242
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 ).
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/
-
¿Faltan episodios?
-
Because only one type of nucleotide is not complicated enough
Chapters:
01:35 Introducing old problems
15:30 More Phred, more better
34:40 QuickGen: genetic testing
47:40 Bioinformatics tools: samtools
PacBio ONSO Specs: https://www.pacb.com/wp-content/uploads/Onso-specification-sheet.pdf
SBB explained by PacBio: https://www.pacb.com/blog/sbb-sequencing/
Why higher quality is better: https://pmc.ncbi.nlm.nih.gov/articles/PMC11331594/
Short read sequencing market heating up: https://www.nature.com/articles/s41587-022-01632-4
SBB for visual learners: https://www.youtube.com/watch?v=i_mSaNBOVmQ
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 ).
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/
-
Mixing up long and cheap
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/
-
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/
-
Getting the most out of Machines
Chapters:
00:00 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 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 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/
-
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 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 at 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/
-
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 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 at 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/
-
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/
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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/
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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/
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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/
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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/
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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 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).
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/
