The Epigenetics Epic - Part 1

A long time coming, but here it is!Introduction: https://medlineplus.gov/genetics/understanding/howgeneswork/epigenome/Mechanisms: https://en.wikipedia.org/wiki/EpigeneticsDNA packaging: https://www.nature.com/scitable/topicpage/dna-packaging-nucleosomes-and-chromatin-310/Chromatin and gene regulation: https://learn.genetics.utah.edu/content/epigenetics/control/Histone writers, erasers and readers: https://www.nature.com/articles/emm201711DNA methylation, DNMTs and SAM: https://www.nature.com/articles/npp2012112Modified bases (5mC, N6-mA): https://en.wikipedia.org/wiki/DNA_methylationActive DNA demethylation (TET/TDG/BER): https://www.tandfonline.com/doi/full/10.1080/17501911.2025.2586452Bisulfite sequencing (WGBS): https://www.illumina.com/techniques/sequencing/methylation-sequencing/bisulfite-sequencing.htmlWGBS alignment benchmarking: https://www.sciencedirect.com/science/article/pii/S2001037022003853Illumina 5-base methylome sequencing: https://www.illumina.com/techniques/sequencing/methylation-sequencing/methylome-genome.htmlMethylationEPIC v2.0 array: https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.htmlInfinium 450K datasheet: https://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/datasheet_humanmethylation450.pdfPacBio HiFi methylation detection: https://www.pacb.com/revio/SMRT direct methylation detection: https://www.pacb.com/publications/direct-detection-of-dna-methylation-during-single-molecule-real-time-sequencing/Fiber-seq and cancer research: https://www.pacb.com/blog/what-a-clearer-view-of-epigenetics-can-mean-for-cancer-research/PacBio epigenetics overview: https://www.pacb.com/products-and-services/applications/epigenetics/Sequencing 101: Epigenetics: https://www.pacb.com/blog/sequencing-101-epigenetics/Oxford Nanopore modified-base calling: https://nanoporetech.com/applications/investigations/epigenetics-and-methylation-analysisNanopore sequencing accuracy: https://nanoporetech.com/platform/accuracyNanopore chromatin accessibility (EPI2ME): https://epi2me.nanoporetech.com/chromatin-acc-hg002/Nanopore 5mC/5hmC detection: https://www.nature.com/articles/s42003-025-07681-0Ultima Genomics (bisulfite, EM-seq, TAPS+): https://www.ultimagenomics.com/focus-areas/methylation-profiling/Watchmaker TAPS+: https://www.watchmakergenomics.com/taps.htmlElement AVITI methylation sequencing: https://www.elementbiosciences.com/applications/dna-sequencing/methylation-sequencingMGI DNBSEQ bisulfite sequencing: https://link.springer.com/article/10.1186/s13148-023-01543-4NEBNext EM-seq v2: https://www.neb.com/en-us/products/e8015-nebnext-enzymatic-methyl-seq-v2-kitNEBNext enzymatic 5hmC-seq: https://www.neb.com/en-us/products/e3350nebnext-enzymatic-methyl-seq-5hmc-kit5hmC detection overview: https://www.neb.com/en-us/products/epigenetics/methylation-analysis/5hmc-hydroxymethylationmeCUT&RUN: https://www.epicypher.com/product/cutana-mecutrun-kit-for-dna-methylation-sequencing/Fiber-seq chromatin profiling: https://www.epicypher.com/fiber-seq-long-read-sequencing/Fiber-seq + PacBio HiFi: https://www.pacb.com/blog/how-pairing-epicyphers-fiber-seq-with-hifi-sequencing-delivers-an-all-in-one-multiomic-view/MeDIP: https://www.activemotif.com/catalog/736/medipLINE-1 global methylation assay: https://www.activemotif.com/catalog/1043/global-dna-methylation-assay-line-1RRBS: https://www.nature.com/articles/nprot.2010.190DNA methylation biomarkers in liquid biopsies: https://www.nature.com/articles/s41388-025-03624-5Listen to our podcast and we're happy to receive your feedback&questions via Email (podcast[dot]explain[at]gmail[dot]com ).Podcast Title: Explain PodcastCreators: Iuliia Novoselova, Daniel RickertWebsite: ⁠⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

The open-source DIY Sequencer was here.Update: 454.bio is now dead, but the archives still have it: https://web.archive.org/web/20250723191639/https://454.bio/Their GitHub:https://github.com/454bioElements new VITARI: https://www.elementbiosciences.com/products/preorder-vitari

We have the same thing at home!- yes, but in worse, cheaper or bothQitan:https://pmc.ncbi.nlm.nih.gov/articles/PMC8985760/https://www.qitantech.com/The QPinnacle2: https://www.vcbeathealth.com/article/1821CycloneSEQ, the MGI-internal clone:https://en.cyclone-seq.com/nanopTechhttps://www.prnewswire.com/news-releases/mgi-launches-new-nanopore-sequencing-products-with-advanced-cycloneseq-technology-302241816.htmlhttps://www.biorxiv.org/content/10.1101/2024.08.19.608720v1https://rrwick.github.io/2024/12/17/cycloneseq.htmlhttps://gigabytejournal.com/articles/154https://gigasciencejournal.com/blog/open-cycloneseq-benchmarking-for-complete-bacterial-genomes/Polyseq:https://polyseq.com/Axbio:https://www.axbio.cn/products/45.htmlGeneus-tech:http://www.geneus-tech.com/proddetail.aspx?id=1Nice not up-to-date table of specs:https://github.com/zhangtianyuan666/NanoporeReview2024ONT to double promethion throughput: https://www.genomeweb.com/sequencing/jpm-oxford-nanopore-shares-plans-double-flow-cell-output-expand-menu-biopharma-market

Artificial Intelligence everywhere, and sometimes its useful.Correction: apparently the Biostar Handbook is not free anymore :(AlphaGenome:https://omicsomics.blogspot.com/2026/02/non-coding-dnas-alpha-moment.htmlhttps://www.alphagenomedocs.com/installation.htmlhttps://www.genomeweb.com/informatics/google-alphagenome-users-scrutinize-ai-models-ability-predict-variant-effectshttps://deepmind.google.com/science/alphagenome/Bioinformatics Forums:Bioinformatics mistakes on Biostars: https://www.biostars.org/p/7126/Bioinformatics stackexchange:https://bioinformatics.stackexchange.com/Seqanswers:https://www.seqanswers.com/forum/sequencing-technologies-companiesVibecoding (current setup, top to bottom):https://claude.ai/newhttps://gemini.google.com/apphttps://duck.ai/If danger is something you enjoy, use this: https://openclaw.ai/YOU HAVE BEEN WARNEDPaper about old LLMs that can solve simple, old and solved bioinformatics problems:https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011511Youtube has useful bioinformatics courses:1: https://www.youtube.com/watch?v=3XFpxQF0J74&list=PLWVKUEZ25V95IKyBrxHtRTK_6Ig8Xi9-f2: https://www.youtube.com/watch?v=LvtPXZHNoCc&list=PLeB-Dlq-v6taAXK6ZCGfqImrNWJzFt3p3

When do you get your Illumina sticker for your ONSO? This is the first part of a two-parts news roundup.PacBio News:https://aseq.substack.com/p/pacbio-sells-short-read-tech-to-illuminahttps://www.pacb.com/press_releases/pacbio-completes-sale-of-short-read-sequencing-assets/https://albertvilella.substack.com/p/pacbio-sells-short-read-ip-to-illuminaThe 6-base sequencing run:https://www.pacb.com/wp-content/uploads/PAG-5hmC-Portik.pdfhttps://www.nature.com/articles/s42003-025-07681-0ONT's P2 solo drama:https://omicsomics.blogspot.com/2026/01/p2-solo-ont-extends-support-but-not.html

For when matching and sticking is enough to getLinks:Nice Youtube explainer: https://www.youtube.com/watch?v=NgRfc6atXQ8Another nice one: https://www.youtube.com/watch?v=4bOY2Oh5tEQExplaining this and more: https://berkeleygenomics.org/articles/How_many_human_genomes_have_been_sequenced_.htmlSince 2018, the West German Genome Center (⁠https://wggc.de/⁠) 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 NoticeThis 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 PodcastCreators: Iuliia Novoselova, Daniel RickertWebsite: ⁠⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

After 454 now the second try by Roche: Axelios.Preprint: https://www.biorxiv.org/content/10.1101/2025.02.19.639056v1Read here about the PoC: https://www.pnas.org/doi/full/10.1073/pnas.1601782113Current state (2025): https://www.nejm.org/doi/full/10.1056/NEJMc2512825Correction: the 5B flow cell will arrive for the NovaseqX(+), not for the Nextseq2000Also:PacBio makes sequencing cheaper: https://www.pacb.com/press_releases/pacbio-announces-major-advances-for-revio-and-vega-to-lower-genome-cost-and-expand-multiomic-capabilities/⁠Roche about SBX: https://sequencing.roche.com/global/en/article-listing/sequencing-platform-technologies.htmlRoche from a conference: https://www.youtube.com/watch?v=YN2meswiCiQSince 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 NoticeThis 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 PodcastCreators: Iuliia Novoselova, Daniel RickertWebsite: ⁠⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

This time something different.Sources:https://www.23andme.com/privacy/https://verbraucherschutzforum.berlin/2025-03-25/23andme-meldet-insolvenz-an-was-nutzer-jetzt-wissen-sollten-357738/https://en.wikipedia.org/wiki/23andMe_data_leakhttps://www.cshub.com/attacks/news/23andme-hacker-leaks-datahttps://www.cbsnews.com/news/dna-privacy-at-home-tests-23andme-ancestrydna-sell-data-to-third-parties/https://techcrunch.com/2025/03/24/23andme-faces-an-uncertain-future-so-does-your-genetic-data/https://www.theverge.com/2024/9/13/24243986/23andme-settlement-dna-data-breach-lawsuithttps://newsroom.regeneron.com/news-releases/news-release-details/regeneron-enters-asset-purchase-agreement-acquire-23andmer-256/

The science of white blood cells, and much moreChapters:05:30 Immunology how?22:05 22q11.2 deletion syndrome34:30 Scientific collaboration40:00 Data losses50:00 Flip it!53:00 outlook 2030Links:mini-immunology intro:https://www.youtube.com/watch?v=k9QAyP3bYmc22Q e. V. - zentraler Anlaufpunkt für Menschen mit Deletionssyndrom 22q11 oder Duplikationssyndrom 22q11 im deutschsprachigen Raum https://www.wirsind22q.de/aus-dem-verein/vorstandPodcast for young immunologists from young immunologists https://theyoungimmunologist.buzzsprout.com/Contact Nora here https://www.linkedin.com/in/nora-balzer-phd-253a767bSome information about training courses and events https://www.immunology.org/traininghttps://dgfi.org/dgfi-en/academy-of-immunology/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 NoticeThis 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 PodcastCreators: Iuliia Novoselova, Daniel RickertWebsite: ⁠⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

Sharing a flowcell, reinventedChapters:- 00:00 usegalaxy.org- 07:55 Singular Genomics start- 21:55 Max Reads- 29:40 DNA Structure / ATAC-seqSetup galaxy on local hardware: https://galaxyproject.org/admin/get-galaxy/G4 is competing with Illumina:https://www.genengnews.com/topics/omics/fast-and-flexible-singulars-g4-takes-aim-at-illuminas-sequencing-superiority/Singulars chemistry is one of many:https://www.nature.com/articles/d41586-023-00512-4How max reads works:https://techwriting.singulargenomics.com/max-read/Max-Read-Kit-User-Guide-600026.pdfSmall intro to DNA Structures:https://en.wikipedia.org/wiki/Nucleic_acid_quaternary_structureIntro to ATAC-seq:https://www.nature.com/articles/s41596-022-00692-9PS:As of 2025, Singular does not advertise DNA/RNA Sequencing on their G4 anymore, but shifted to spatial data, including their G4X: https://www.singulargenomics.com/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 NoticeThis 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 PodcastCreators: Iuliia Novoselova, Daniel RickertWebsite: ⁠⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠