Jan 31, 2023 / Oncology / Immunology / Neuroscience / Developmental Biology / Software

Innovative and effortless: How 10x Genomics makes hard things easy

Josh Azevedo

It happens more often than it should: a researcher is interested in a cutting-edge method, they look into it, then they move on because the difficulties seem to outweigh the rewards. Maybe it’s too technically demanding for the data it provides or it requires in-depth training because the lab doesn’t have experience with it (and that’s usually enough for Reviewer 2 to reject the funding application).

That’s always struck us as inefficient because technology only benefits you if it’s actually usable. Our philosophy is that cutting-edge technology should be more accessible, and fostering that requires us to make difficult things easy. So we spent our 2022 listening to your challenges, concerns, and pain points, and we want to start this year showcasing what that taught us—and how it can help you. Read on to see how we can help your lab take the next leap forward in 2023 with innovative technology made effortless!

Building (or diversifying) single cell technologies in your lab

One of the best parts of being a scientist is getting to use a new approach to answer those nagging questions—but incorporating it into the lab can be one of your biggest challenges. It goes beyond just getting the protocol to work: optimizing the protocol for your specific needs, making sure everyone is trained on it, and learning how to analyze new kinds of data are non-trivial aspects when using single cell sequencing.

For those looking to try out one (or several!) single cell technologies with minimal commitment, we’ve partnered with a number of core labs at universities around the world: just drop off your samples and they’ll take care of the rest. Best of all, no bioinformatics experience is required: just load your data into our Cell Ranger software suite and immediately explore your results with the intuitive and user-friendly Loupe Browser.

If your lab is interested in making single cell sequencing part of your routine toolkit, all of our single cell gene expression, ATAC, immune profiling, and multiomic technologies feature easy end-to-end workflows that require minimal training and hands-on time. Our expert support staff can get you up and running and help you optimize your assays for your starting samples—even for challenging ones like FFPE tissues (and other samples with damaged or degraded RNA).

We also have you covered if your lab wants to try something new: the same instrumentation can let you tailor your experimental throughput to your needs (all the way up to multi-site studies). Even better, our single cell assays all use similar workflows and run on the same equipment, meaning a one-time investment in instrumentation lets you expand your approaches and look at your samples in a whole new light.

Minimizing artifacts by locking in cell state

Single cell experiments require you to dissociate your tissue into a single cell suspension. While this is theoretically simple, it can be very challenging in practice: even ignoring that certain tissues (such as pancreas and brain) can be difficult to work with, some dissociation methods may introduce bias that can affect the identification of cell type. This is difficult enough in a single lab, but it can significantly impact large-scale or multi-site studies that require prompt dissociation with extended storage and/or transportation.

To address these challenges, we spent our 2022 demonstrating the expanded capabilities of our Chromium Single Cell Gene Expression Flex assay, which enables single cell gene expression analyses on not just fresh samples, but on PFA-fixed and FFPE cells and tissue. Fixing samples at the point of collection allows you to lock in cell state, eliminating dissociation-induced bias and capturing an immediate “snapshot” of the cell at the time of collection.

How can this make your life easier? For starters, by expanding your sample access. With robust and validated protocols that provide compatibility with PFA and FFPE, Flex lets you use biobanked and archival samples for your study, letting you access hundreds to thousands of samples rather than being limited to the availability of fresh tissue. Compatibility with PFA fixation also enables you to decouple tissue collection from tissue processing, giving you the option to “batch” samples together to minimize technical artifacts—a feature that is particularly useful for multi-site and/or large-scale studies. These batching and time-insensitive capabilities also help smaller labs, or those with unpredictable sample collection times, to minimize variability and run their studies on their schedule.

See more spatial with Visium CytAssist

The spatial “where” of gene expression has lagged behind the cellular “what” provided by single cell because spatial transcriptomics requires a different—and more challenging—approach. We’re immensely proud to be one of the driving forces in spatial transcriptomics technologies, but some persistent challenges—such as tissue placement and identifying regions of interest for further analysis—have remained.

To address these pain points, we introduced Visium CytAssist last year. This compact, benchtop system takes our standard Visium Gene Expression assays and makes them even better: not only can you continue to section FFPE sections from blocks onto the slides, but CytAssist now lets you use pre-sectioned FFPE and fresh frozen tissue on standard glass slides for Visum workflows.

Visium CytAssist can easily integrate into familiar standard histology and immunofluorescence workflows with minimal training required. More importantly, in addition to enabling the use of pre-sectioned FFPE and fresh frozen tissues, it allows tissue sections to be pre-screened and pre-aligned, allowing you to select only optimal tissue sections for further downstream analysis.

Do more, more easily, in 2023

A new year means new work in the lab, and you can resolve to make it easier by adding new single cell assays, more flexible single cell RNA-seq, streamlined spatial transcriptomics, and more. We’re constantly working on that “more” for the new year, so stay tuned! In the meantime, take the next step and jump start your work with the Oncology and Neuroscience Foundational Guides, or the Immunology eBook.