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Koen De Gelas @kdegelas.bsky.social · 2d

This 100%

Marco Breinig @breinigmarco.bsky.social · 2d

Co-mapping clonal and transcriptional heterogeneity in somatic evolution via GoT-Multi

Pak, Saurty-Seerunghen et al. present a method, GoT-Multi, that co-detects single-cell multiplexed somatic genotyping and whole transcriptomes in high throughput from fresh or FFPE samples, overcoming...

www.cell.com

Koen De Gelas @kdegelas.bsky.social · 26d

Its not possible to send a DM

Koen De Gelas @kdegelas.bsky.social · 28d

Concluding remarks by the authors part 2: "The Flex workflow proved to be amenable to sample collection at the clinical site, making it the best choice for implementation in clinical trials."

Koen De Gelas @kdegelas.bsky.social · 28d

Concluding remarks by the authors: "We determined that Flex exhibited the best performance, with the proportions of neutrophils captured in blood samples comparable to those observed by flow cytometry."

Koen De Gelas @kdegelas.bsky.social · 28d

Another independent benchmarking study, this time on neutrophils. Comparing 10X 3 prime, 10X Flex, Parse Evercode and Hive.
www.cell.com/cell-reports...

Comparison of single-cell RNA-seq methods to enable transcriptome profiling of neutrophils in clinical samples

Hatje et al. evaluate current fixed single-cell technologies to determine their suitability for measuring the neutrophil transcriptome and their potential for implementation in clinical trials.

www.cell.com

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Reposted by Koen De Gelas

Alexandra P @alexanrna.bsky.social · Sep 10

1/ First preprint from @jdemeul.bsky.social lab 🥳! We present our new multi-modal single-cell long-read method SPLONGGET (Single-cell Profiling of LONG-read Genome, Epigenome, and Transcriptome)! www.biorxiv.org/content/10.1...

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Reposted by Koen De Gelas

10x Genomics @10xgenomics.bsky.social · Sep 9

Imagine detecting bone marrow disorders without a painful aspiration! The PERIBLOOD clinical trial by CLISEQ Ltd., the Weizmann Institute of Science & Weizmann’s commercial arm Yeda will see if a blood draw & GEM-X #scRNAseq could help develop future diagnostics. https://bit.ly/46i7TrX

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Reposted by Koen De Gelas

10x Genomics @10xgenomics.bsky.social · Aug 14

✨ Join us on August 28 for an educational webinar that covers the #Xenium workflow, including new features of the platform and expert tips and tricks 🔬 Learn more and reserve your spot here: bit.ly/3U2D5FT

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Koen De Gelas @kdegelas.bsky.social · Aug 14

Yes, you can use @10xgenomics.bsky.social Xenium high resolution transcriptomics on plants. Jhu et al. wrote a "how-to-guide" with specific protocol modifications. Medicago truncatula roots and nodules FFPE tissue, 480 genes. Check it out here: www.biorxiv.org/content/10.1...

Plant-Compatible Xenium In Situ Sequencing: Optimised Protocol for Spatial Transcriptomics in Medicago truncatula Roots and Nodules

Elucidating the spatial and temporal regulation of gene expression during plant organogenesis is crucial for enabling precise crop improvement strategies that incorporate beneficial traits into crops ...

www.biorxiv.org

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Koen De Gelas @kdegelas.bsky.social · Aug 7

What a cool paper!

Stegle Lab @steglelab.bsky.social · Aug 7

A scalable framework enabling the induction and spatial genotyping ➡ phenotyping of hundreds of tumors in mouse liver. #CHOCOLAT-G2P

Check out the publication for the nuts and bolts of 🍫-G2P: doi.org/10.1038/s415...

Moritz Gerstung @moritzgerstung.bsky.social · Jul 29

This is a great set of methods for studying combinatorial effects of cancer mutations on spatial phenotypes.

Clever experimental design by @breinigmarco.bsky.social hijacking Visium and elegant analysis by @lomakinai.bsky.social and @elihei.bsky.social

www.nature.com/articles/s41...

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Koen De Gelas @kdegelas.bsky.social · Aug 7

This is SO COOL!

Koen De Gelas @kdegelas.bsky.social · Jul 29

New preprint by M4I, Maastricht, The Netherlands integrating high-resolution MALDI-MSI with Xenium single cell spatial transcriptomics on one single tissue section. www.biorxiv.org/content/10.1...

One Section, Two Worlds: Single-Cell Integration of MALDI-MSI and Spatial Transcriptomics on the Same Single Tissue Section

Understanding tissue complexity requires spatially resolved multiomic data at single-cell resolution. Here, we present a workflow that integrates high-resolution matrix-assisted laser desorption ioniz...

www.biorxiv.org

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Koen De Gelas @kdegelas.bsky.social · Jul 28

Want to learn more about high resolution, high plex spatial transcriptomics? New 10X Genomics Xenium educational webinar on Thursday Aug 28, 2025 ⋅ 15:00 – 16:00 (Central European Time - Brussels).
Register here: bit.ly/4fjtYKM

10x Genomics

bit.ly

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Reposted by Koen De Gelas

10x Genomics @10xgenomics.bsky.social · Jul 22

New on Xenium: validated & ready-to-use protein panels! Now you can analyze 27 proteins alongside #spatial RNA for multiomic insights into #cancer, #immunology & more. Get a hands-on look with our interactive dataset & then pre-order your assay: bit.ly/4o0896R

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Koen De Gelas @kdegelas.bsky.social · Jun 23

Highly recommended read if you are looking into spatial transcriptomic options.

Karsten Rippe @karsten-rippe.bsky.social · Jun 20

1/ Spatial transcriptomics technologies are rapidly evolving. We compared five methods—Visium, RNAscope HiPlex, Molecular Cartography, Merscope, and Xenium—and developed technology-agnostic quality control metrics to guide their use: doi.org/10.1186/s130...

Comparison of spatial transcriptomics technologies using tumor cryosections - Genome Biology

Background Spatial transcriptomics technologies are revolutionizing our understanding of intra-tumor heterogeneity and the tumor microenvironment by revealing single-cell molecular profiles within the...

doi.org

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Reposted by Koen De Gelas

10x Genomics @10xgenomics.bsky.social · Jun 12

Join our webinar on the new #VisiumHD 3’ assay to explore spatial transcriptomics and the technical aspects of the platform. This session offers practical insights and examples for both beginners and experienced users looking to optimize spatial experiments. Register at bit.ly/3How6E6

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Koen De Gelas @kdegelas.bsky.social · Jun 12

@10xgenomics.bsky.social spatial transcriptomics Visium HD 3 prime assay is shipping! Get whole transcriptome gene expression data at a resolution of 2x2µm. Poly A based, species agnostic. Compatible with short and long read sequencing.
Check it out here:
www.10xgenomics.com/products/hd-...

Visium HD 3’ - 10x Genomics

Next-generation Visium HD technology–powered assay with whole transcriptome coverage to gather broad information from diverse species.

www.10xgenomics.com

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Reposted by Koen De Gelas

10x Genomics @10xgenomics.bsky.social · Jun 11

We’re shipping the #VisiumHD 3’ assay! Learn how to bring species-agnostic, whole transcriptome spatial analysis at single cell scale to your lab, including new cell segmentation capabilities compatible across all HD products: bit.ly/4mPrGX5

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Reposted by Koen De Gelas

Ming Tommy Tang @tommytang.bsky.social · Jun 7

You’re analyzing 10x Genomics single-cell RNA-seq and notice lots of intronic reads.
Wait—wasn’t this a 3′ UMI-based assay for mature mRNA?
Let’s unpack why introns show up—and why they matter. 🧵

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Koen De Gelas @kdegelas.bsky.social · Jun 6

Read the blog to learn how 10x scientists used the #Chromium single cell, #VisiumHD and #Xenium platforms in human colorectal cancer to localize anti-tumor macrophage subtypes and clonally expanded T cells in the TME: bit.ly/4439Xnu

How mapping the spatial biology of the tumor microenvironment can benefit cancer drug discovery and development - 10x Genomics

Spatial transcriptomics reveals complex and therapeutically relevant interactions among tumor and immune cells in the TME and tumor boundary.

bit.ly

Koen De Gelas @kdegelas.bsky.social · Jun 6

New @NatureGenetics paper! 🧬🔬 High-res spatial transcriptomics of #CRC reveals distinct macrophage types & T cell interactions. Using Visium HD, this work deepens our understanding of the tumor microenvironment to improve #colorectalcancer treatment.

Full paper: www.nature.com/articles/s41...

High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer - Nature Genetics

High-resolution, spatial transcriptomic analysis of colorectal cancers using matched sequencing- and imaging-based methods characterizes immune cells and their interactions with the tumor microenviron...

www.nature.com

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Koen De Gelas @kdegelas.bsky.social · Jun 5

Introducing the Visium HD 3’ assay, whole transcriptome spatial analysis with 3’ poly(A) capture-based chemistry.
Spatial biology of fresh frozen samples from any species
De novo discovery, including isoforms, TCRs/BCRs, and SNVs
Single cell resolution, new cell segmentation software
bit.ly/43ROP2r

10x Genomics

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Reposted by Koen De Gelas

10x Genomics @10xgenomics.bsky.social · May 23

Interested in #spatialtranscriptomics but not sure where to start? Don’t worry, Dr. Porta-Pardo and Daniela Grases wrote the guide for that. Learn how to select the right platform, optimize your experiments, and scale up your studies. Read it now: www.preprints.org/manuscript/2...

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Koen De Gelas @kdegelas.bsky.social · May 25

New independent single cell benchmarking study by the @fredhutch.bsky.social innovation lab. Check it out! www.biorxiv.org/content/10.1...

www.biorxiv.org

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Reposted by Koen De Gelas

Linda Kvastad @kvastad.bsky.social · May 22

Recently presented our work on how spatial transcriptomics + genetics can reveal putative causal tissue structures for complex traits.
📄 Preprint: doi.org/10.1101/2025...
#spatialbiology #genomics #genetics @lifesciences-ge.bsky.social

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