Hosted by: Catia Moutinho & Tommy Tang Guest: Jonathan Alles, Founder of EVOBYTE Digital BiologyIn this episode, Jonathan tells us how EVOBYTE’s EVO Data platform is revolutionizing data management for research labs, with a focus on single-cell research. Our conversation covers EVOBYTE’s unique solutions, customization capabilities, practical applications, and the role of automation in bioinformatics workflows. Jonathan also shares his insights on the future of computational biology and advice for budding bioinformaticians.Links that may interest you:* Introducing EvoData Platform* ReadStore is a platform for storing, managing, and integrating genomic data. It speeds up analysis and offers a secure way of managing and sharing FASTQ and NGS datasets. 30 DAY FREE TRIAL DEMO.Enjoy the episode! This is a public episode. If you would like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com
In this podcast episode, I talk with Francesca Giannese about an exciting new method for studying chromatin at the single-cell level called scGET-seq. Unlike previous methods such as scATAC-seq, which only allow us to study open chromatin, scGET-seq provides insights into both open and closed chromatin. This breakthrough can lead to a deeper understanding of how chromatin structure impacts gene regulation in individual cells. Tune in to learn more about how scGET-seq works and its potential applications in research.Contacts for support on scGET-seq implementation:* Francesca Giannese (wet-lab protocol implementation - enzyme requests)* Davide Cittaro (data analysis)More information about scGET-seq* scGET-seq Wikipedia * Original PaperData Analysis* Analyzing genomic and epigenetic profiles in single cells by hybrid transposase (scGET-seq)* Analysis and modeling of scGET-seq data Application* Cancer evolution (EMT in pancreatic cancer) This is a public episode. If you would like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com
This episode features the audio from an interview where Divya Dhasman from GenoWrite speaks with Catia Moutinho. They discuss the evolution of The Single-Cell World and explore the role of technology in advancing genomics. Special thanks to Paul Naphtali for making this interview possible. Catch the full interview here.Thanks to you for listen. Hit the ❤️ if you liked it and share it with your colleagues. This is a public episode. If you would like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com
In this episode, I speak with Shuwen Chen, a product manager at Takara Bio, who provides an in-depth look at the various solutions they offer for single-cell research projects. We discuss the Smart-Seq kits, explore their single-cell platforms, and dive into the latest Shasta kits for RNA and DNA. Tune in to find out if these innovative solutions can enhance your research projects.Useful links* Arc-well: a new method for single-cell DNA-seq analysis of formalin-fixed paraffin-embedded samples* CUT&Tag for efficient epigenomic profiling of small samples and single cells* Support this podcast. 👉🏻Pay us a Ko-fi This is a public episode. If you would like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com
In this episode, I talk with Adrian Zambrano, Customer Success Manager at CYTENA. We’ll discuss instruments that can be used in single-cell projects, including upstream tools like single cell dispensation instruments and downstream solutions like automatic bead clean-up.Discover innovative solutions from CYTENA that could enhance your research projects. Tune in to learn how these tools can make our lab work easier and more efficient.Useful links* Resources Cytena* Support this podcast. 👉🏻 Pay us a Ko-fi This is a public episode. If you would like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com
BD Biosciences, known for their cytometers, also offers impressive single-cell sequencing solutions. Today’s guest is Hasi Patel, Senior Single Cell Solutions Architect, who tells me everything about this technology during this episode.Hasi starts explaining how BD's latest high-throughput single-cell platform works, as well as all the multiomics approaches that can be done with their innovative solutions. In all of them, sample multiplexing is possible, enhancing its versatility. Hasi also shares valuable tips on planning single-cell sequencing experiments. Tune in now to learn more about BD Biosciences' innovations in single-cell sequencing!Useful Links:* More information: multiomics.europe@bd.com* Support our podcast and subscribe to our newsletter. This is a public episode. If you would like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com
In this episode, Irene González, the International Key Account Manager at Arrays For Cell Nanodevices, SL (A4cell), discusses their microdevices known as SPAchips. She explains how these devices allow us to directly measure various characteristics in living cells, such as reactive oxygen species (ROS), calcium and pH levels.A4Cell email: info@a4cell.comSupport our podcast: pay us a Ko-fi This is a public episode. If you would like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com
Join me, Cátia Moutinho, as I break down the basics of spatial transcriptomics legal battles ⚖️ between companies in this field. I'll share my opinions 💭, propose solutions 🛠️, and raise open questions ❓ that might have you thinking. This is a message for judges, companies teams and researchers. 😉Tune in now! 🎧The Single-Cell World Blog, Newsletter.Pay us a Kofi This is a public episode. If you would like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com
In this episode, Ritika Kulshreshtha, Singleron Account Manager, tells me everything about their different kits for single cell experiments. For example, a kit to study DNA and RNA in parallel, another to study glycosylation, mRNA from yeast, or nascent RNA. So, if you are interested in doing novel single cell experiments, listen to this episode now!Useful links:Singleron Boot CampSupport our Podcast (2$ per month) This is a public episode. If you would like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com
Hi there 👋 The topic of this episode is VASA-seq, a single-cell transcriptomics method that we can use to study coding and non-coding RNA. Listen now to my conversation with Fredrik Salmén, the first author of the paper where VASA-seq is described. He gives me an amazing explanation about this method, besides his opinion on other topics related to single-cell and spatial experiments. You will not want to skip this one!Other useful links:* Pay us a Ko-fi* SORT-seq* Atrandi Biosciences* Single Cell Discoveries* Genevia Technologies This is a public episode. If you would like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com
In this podcast episode, I have the pleasure of talking with Kevin Travers, the Senior Vice President for R&D at LevitasBio.Kevin tells me everything about their gentle and label-free technology that can be used during sample preparation for any single cell sequencing experiments, but also for other downstream applications.🎧Tune in now and learn how levitation technology can make your experiments better.✨Useful Links:* Levitation Technology for Single Cell Genomics* The LeviCell Systems for Cell Isolation and Enrichment This is a public episode. If you would like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com
Join us on this podcast episode as I explore the fascinating world of single-cell RNA sequencing (scRNA-seq) data normalization with Amartya Singh, a post-doctoral researcher at Reuters. Discover the limitations of the standard methods used in scRNA-seq data normalization and how Amartya's innovative solution is changing the game. Hear firsthand about his journey of inspiration and the ideas that led to the development of this groundbreaking approach. Don't miss out on this insightful discussion - tune in now!Useful Links:* Amartya Singh LinkedIn and GitHub profile* The starting point publication * TuBA paper* Piccolo paper❤️ Support our podcast: pay us a Ko-fi This is a public episode. If you would like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com
In this insightful podcast interview with Kieren Patel, the Chief Business Officer at Resolve Biosciences, we delve into the world of Molecular Cartography technology. Kieren provides details about this innovative platform, underscoring its remarkable capabilities in facilitating high molecular resolution pathology. Additionally, Kieren sheds light on forthcoming solutions set to be commercialized later this year, with a particular emphasis on their commitment to multiomics and customized approaches. Tune in to gain valuable insights into the latest advancements in molecular cartography and discover the promising future that Resolve Biosciences' offerings hold.Useful links:Resolve Biosciences * website* LinkedIn* Twitter* Youtube* DatasetsKieren PatelSupport our podcast: pay us a Ko-fi This is a public episode. If you would like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com
In this podcast episode, I had the privilege of talking with Melanie Masuda, the Director of Market Development at Scale Biosciences. Melanie told me all about Scale Biosciences' cutting-edge technology and gave me a full overview of all of their different kits.Listen now and understand how the single-cell (sc) sequencing DNA methylation, the scRNAseq, and the CRISPR enrichment kits work. Maybe this is the solution for your research project!Useful Links:Melanie Masuda LinkedInScale Biosciences(website)* Twitter* LinkedInKITS* scDNA methylation* scRNA* CRISPR guide enrichment kitSupport our podcast: pay us a Ko-fi This is a public episode. If you would like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com
In this insightful podcast episode, I have the privilege of interviewing Simone Picelli, the Head of the Single-Cell Genomics Platform at the Institute of Ophthalmology Basel. As we talked, we got into the specifics of single-cell RNA sequencing (scRNA-seq) full-length methods from the SMART-seq family.Simone shared valuable insights into various methods within, including SMART-seq, SMART-seq 2, SMART-seq 3, FLASH-seq, FLASH-seq low-amplification, and FLASH-seq with UMI. We explored the unique features and applications of each method, highlighting their contributions to advancing single-cell genomics research. In addition, we also talked about other common methods and the bigger picture of single-cell sequencing technology, such as the problems it faces and its future.Explore the fascinating world of SMART-seq methods with Simone Picelli - a must-listen episode. Tune in now and learn about the ideal way to study RNA isoforms. ----more----USEFUL LINKS:* Simone Picelli Information* LinkedIn* LaboratoryPublications* SMART-Seq* SMART-Seq 2 Original Paper* SMART-Seq 2 Method Paper* SMART-seq 3* SMART-Seq 3 Express* FLASH-seqProtocols:* FLASH-Seq* FLASH-Seq UMI* FLASH-Seq low amplification* Bulk FLASH-SeqScientist.com: science as a serviceSupport our podcast: pay us a Ko-fi This is a public episode. If you would like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com
The Single-Cell World Podcast is now available in video as well, but just on Apple Podcast and in our new YouTube channel 😉Episode 14: Single-Cell Methods, an overview, needed an update since there is a fourth method that is being used to individualize cells when using single-cell sequencing technology.Join me and listen to it, as well as other updates concerning the methods that are at the core of the single-cell sequencing technology.Here I leave you a gift, related with this episode.Thank you for listening.Kind Regards,Cátia This is a public episode. If you would like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com
Hi there!Today is Part 2 of the review of single-cell-related products launched in 2023. I hope I don't miss any. If I do, send me a message telling me about it. 😉Here are some useful links:Exploring Single-Cell Sequencing online courseCompanies that I talk during this episode (part 2):Scale BiosciencesScipio BioscienceSingleron BiotechnologiesTakara Bio10X GenomicsFree ResourcesSponsorshipPay me a Ko-FiThanks for listening!Cheers,Cátia This is a public episode. If you would like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com
Hi there!Today I review single-cell-related products launched in 2023. They are a lot! I hope I don't miss any. If I do, send me a message telling me about it. 😉Here are some useful links:Join the Single-Cell World NewsletterCompanies that I talk during this episode (part 1):BD Biosciences Ep. 18: Samples MultiplexingBioScryb GenomicsFluent BioSciencesEpisode 31: Podcast Fluent BioSciencesHoneycomb BiotechnologiesEpisode 19: Podcast Honeycomb BiotechnologiesMission BioEpisode 16: Podcast Mission BioParse Biosciences Episode 35: Podcast Parse BiosciencesFree ResourcesSponsorshipPay me a Ko-FiThanks for listening!Cheers,Cátia This is a public episode. If you would like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com
Hello there!The Spatial and Single-Cell Analysis Playbook was released last week. Front Line Genomics produced it. I was honored to be invited to take part in it.In this episode, you can hear the questions that were asked (AI voice here) and my responses during this fantastic interview.I hope you like it!Useful LinksFree ResourcesThe Single-Cell World websiteSponsorshipPay me a Ko-FiThanks for listening.Cheers,Cátia This is a public episode. If you would like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com
Hi there!Would you like to know what quality control steps I think are essential before a spatial transcriptomics experiment? In my experience, these control steps can save you a lot of headaches.Listen now, and tell me if you agree.Useful LinksThe Single-Cell World websiteSponsorshipPay me a Ko-FiThanks for listening.Cheers,Cátia This is a public episode. If you would like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com