Industry insights
Publication highlight: Spatial mapping of barcoded, brain-tropic AAVs using multiplexed RNA in situ hybridization
In a recent publication Fouani et al. utilized the 10x Genomics Xenium in situ platform to track a barcoded pool of 22 distinct Adeno-associated virus (AAV) variants within the intact brain. This novel spatial genomics approach allowed them to evaluate the spatial distribution and cellular tropism of gene therapy vectors simultaneously, preserving the crucial anatomical context that traditional sequencing methods lose. in addition, this approach revealed how engineered AAV9 variants differ in their ability to cross the blood-brain barrier, with some showing vascular bias and others preferentially targeting specific neuronal subtypes — opening new possibilities for precision CNS gene therapy vector design.
Key findings
- High-throughput spatial resolution: By leveraging the Xenium platform, the method successfully mapped the molecular identities and exact anatomical locations of 22 different AAV variants at single cell resolution without requiring tissue dissociation.
- Distinct regional tropism: The spatial profiling revealed highly specific, differential distribution patterns among the pool of AAV variants across the brain following systemic delivery.
- Region-dependent cell preferences: The study showed that AAV cell-type targeting shifts depending on the brain region, such as transducing both astrocytes and neurons in the cortex while primarily targeting only neurons in deeper subcortical structures.
Fouani, et al. (2026). Spatial mapping of barcoded brain-tropic AAVs using multiplexed RNA in situ hybridization. Molecular Therapy Advances, 2026; 34 DOI: 10.1016/j.omta.2026.201693
What's new? Meet Atera
On Sunday, April 18, at AACR we announced the arrival of Atera, our new spatial transcriptomics platform. Quoting our CEO, Serge Saxonov: “This is the biggest launch in our history. I am the most excited I’ve ever been about any product, or any product category, across the board,”. Read the full announcement here.
We are immensely proud to introduce this new platform, and we invite you to explore its features through the following resources:
- For the latest information, visit the product page.
- Want to get in touch right away? Speak to Atera sales specialist.
- Watch the webinar — Introducing Atera: Get a firsthand look at uncompromised spatial
Datasets are now available
- Preview Data: Atera In Situ Gene Expression Data for FFPE Human Cervical Cancer
- Interactively explore this dataset with the web demo (click "Open web demo"), a preview of the upcoming desktop version of visualization software.
- Preview Data: Atera In Situ Gene Expression Data for FFPE Human Breast Cancer
Atera World Tour 2026
In science, seeing is believing, and there’s no substitute for seeing what you thought was impossible happen right before your eyes. We invite you to join us on a stop of the 10x Genomics World Tour, where you can:
- See the data from early-access customers and hear about their experience with Atera.
- Get your questions answered by our R&D and senior leadership
Upcoming dates: May 12, 2026 Cambridge | May 13, 2026 Oxford | May 14, 2026 Glasgow | May 18, 2026 Aachen | May 19, 2026 Paris | May 20, 2026 Copenhagen | May 21, 2026 Stockholm | June 17, 2026 Lausanne | June 23, 2026 Barcelona | June 24, 2026 Milan | June 30, 2026 Zurich
Resource hub
This time, we bring you a selection of resources that cover sample prep. See:
- Single Cell FFPE Tested Tissues, using GEM-X Flex and GEM-X Flex v2 (Flex Apex)
- Single Cell Flex Tested Tissues, using GEM-X Flex or GEM-X Flex v2 (Flex Apex) Gene Expression and Next GEM Flex Gene Expression
- Plate-based sample handling and a new era of scale
Webinar recordings
Did you know that all our webinars are available to watch on-demand? Here's a selection of our webinars covering new products, opportunities for translational research, and more:- Flex technology: Performance and application to overcome challenges in clinical trial samples. Speaker: Martina Antoniolli, Ph.D., Research Project Fellow, pRED Oncology, Roche
- Introducing Atera: Get a firsthand look at uncompromised spatial, featuring 10x Genomics R&D and senior leadership and early-access customers
- GEM-X Multiome: Bringing next-generation sensitivity and cost efficiency to joint epigenome and transcriptome profiling. Speaker: Dirk Jürgensen, Staff Field Application Scientist, 10x Genomics
Where to meet us
EACR 2026, 08-11 June, Budapest, Hungary
Join us at EACR 2026 in Budapest to explore the latest advances in single cell and spatial biology.
- Visit us at booth #99 to connect with experts, see the Atera instrument and explore spatial and single cell workflows for FFPE
- Join our Industry Symposium on June 9, 14:30–15:15, room F9+F10, and for the expert talks: Decoding tumor-immune circuits in lung cancer by Heidi Haikala (University of Helsinki) and Dissecting colorectal cancer progression in space and time by René-Filip Jackstadt (DKFZ), featuring first scientific data generated on Atera.
- Also join us Wednesday, June 10 during the Poster Sessions in the Poster Area (Hall H), where researchers will present new data generated using 10x Genomics technologies — including GEM-X Flex (Apex) workflows for clinical and FFPE applications.
During ESHG 2026 we are hosting a scientific session, exploring the forefront of high-resolution biology, epigenetics, and precision medicine. Agenda:
- Epigenetic drivers and biomarkers in type 2 diabetes - Charlotte Ling, Lund University Diabetes Centre
- Cell Suspension and Tissues, Fresh Frozen and FFPE: No Sample Is Left Behind with 10x Genomics - Koen De Gelas, 10x Genomics
Struggling with multi-site trial logistics? Join our upcoming sample prep webinar to see how Fixed Whole Blood and FFPE workflows simplify your process — and get your questions answered live by our technical support team.
Voice of 10x technology users
Hear the reactions of early access Atera users, featuring: Peter Skene, Allen Institute; Jan-Philipp Mallm, DKFZ; Hongkui Zeng, Allen Institute
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