Single-Cell World

In today’s episode, the final episode of The Single-Cell World, Cátia makes a surprising confession. Before speaking with today’s guest, she always assumed that the plastic consumables in single-cell and spatial transcriptomics kits were made by the same companies that developed and commercialized the technology.

But, as it turns out, that’s not the case. In fact, many of these critical consumables are produced by specialized manufacturers—like Edge Precision Manufacturing.

To know more about how these essential components are designed and created, Cátia talks with Andrew Kamholz, the CEO of Edge Precision Manufacturing. Together, they explore the fascinating world of plastic consumable manufacturing and the crucial role these specialized companies play in advancing the technology used in cutting-edge research.

Useful Resources

* Edge Precision Manufacturing Website

* Andrew Kamholz, the CEO of Edge Precision Manufacturing

* Edge Precision Manufacturing LinkedIn

Thank you for listening!

This is a public episode. If you'd like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com/subscribe

10x Genomics is world-class for single cell sequencing technology. As the company continues to innovate and launch exciting new products, it can be challenging to stay up to date on the portfolio and technology, even for us experts. In this episode, I talk to Michael Schnall-Levin, Chief Technology Officer and Founding Scientist at 10x Genomics. He shares everything you need to know about their Chromium single cell sequencing solutions. We cover Chromium instruments, new GEM-X assays, pricing updates, and more.

Tune in now and get a clear idea of all the types of experiments that you can do using 10x Genomics technology.

Other useful information:

Use the links below to learn more about the 10x Genomics Chromium Single Cell portfolio and technology:

* Chromium X Series instruments

* Chromium GEM-X technology

* Chromium GEM-X multiplexing

Chromium Single Cell portfolio of assays.

Active links below the table 👇🏻

*Epi products are the same as the legacy products but now have a new name.

* GEM-X Flex Gene Expression

* GEM-X Universal 3' Gene Expression

* GEM-X Universal 5' Gene Expression

* Next GEM Epi ATAC

* Next GEM Epi Multiome ATAC + Gene Expression

🎧 Listen Now!

This is a public episode. If you'd like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com/subscribe

TileDB software is transforming how scientists manage and analyze data. This includes single-cell omics data. In this episode, Tommy Tang and I talk to Aaron Wolen, Principal Software Engineer at TileDB, to explore the unique capabilities of TileDB-SOMA. Aaron breaks down how this specific software addresses the complexities of single-cell sequencing data, offering robust data management, streamlined workflows, and scalable analysis tools tailored to any needs. We discuss its core features, real-world applications, and the transformative impact it has on accelerating scientific discovery in single-cell genomics research.

Tune in now to learn how TileDB-SOMA can help streamline your research and unlock new possibilities in data analysis!

A big thank you to Kristina LeBlanc, Vice President at Notably, who reached out to TSCW team and made this episode happen.

Usefull links:

* TileDB Academy for Single-Cell

* TileDB blog post about single-cell

* Power Spatial Data with TileDB

This is a public episode. If you'd like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com/subscribe

Hosted by: Catia Moutinho & Tommy Tang 

Guest: Jonathan Alles, Founder of EVOBYTE Digital Biology

In 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'd like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com/subscribe

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 Paper

Data 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'd like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com/subscribe

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'd like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com/subscribe

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'd like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com/subscribe

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'd like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com/subscribe

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: [email protected]

* Support our podcast and subscribe to our newsletter.

This is a public episode. If you'd like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com/subscribe

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: [email protected]

Support our podcast: pay us a Ko-fi

This is a public episode. If you'd like to discuss this with other subscribers or get access to bonus episodes, visit thesinglecellworld.substack.com/subscribe