Koen De Gelas
@kdegelas.bsky.social
STA @ 10X Genomics, views my own
Reposted by Koen De Gelas
What if you could simply ask your analysis tools for answers? We’re collaborating with Anthropic to make that happen, working to turn #singlecell & #spatial analysis into a natural conversation, not a coding lesson. Learn more > https://bit.ly/4nkyURZ
October 20, 2025 at 5:14 PM
What if you could simply ask your analysis tools for answers? We’re collaborating with Anthropic to make that happen, working to turn #singlecell & #spatial analysis into a natural conversation, not a coding lesson. Learn more > https://bit.ly/4nkyURZ
This 100%
October 10, 2025 at 9:00 PM
This 100%
Another independent benchmarking study, this time on neutrophils. Comparing 10X 3 prime, 10X Flex, Parse Evercode and Hive.
www.cell.com/cell-reports...
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
September 15, 2025 at 5:06 PM
Another independent benchmarking study, this time on neutrophils. Comparing 10X 3 prime, 10X Flex, Parse Evercode and Hive.
www.cell.com/cell-reports...
www.cell.com/cell-reports...
Reposted by Koen De Gelas
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...
September 10, 2025 at 3:48 PM
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...
Reposted by Koen De Gelas
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
September 9, 2025 at 5:05 PM
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
Reposted by Koen De Gelas
✨ 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
August 14, 2025 at 10:43 AM
✨ 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
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
August 14, 2025 at 8:38 AM
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...
What a cool paper!
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...
Check out the publication for the nuts and bolts of 🍫-G2P: doi.org/10.1038/s415...
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...
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...
August 7, 2025 at 8:24 AM
What a cool paper!
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
July 29, 2025 at 8:48 AM
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...
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
Register here: bit.ly/4fjtYKM
10x Genomics
bit.ly
July 28, 2025 at 1:30 PM
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
Register here: bit.ly/4fjtYKM
Reposted by Koen De Gelas
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
July 22, 2025 at 3:56 PM
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
Highly recommended read if you are looking into spatial transcriptomic options.
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
June 23, 2025 at 10:53 AM
Highly recommended read if you are looking into spatial transcriptomic options.
Reposted by Koen De Gelas
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
June 12, 2025 at 7:25 AM
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
@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-...
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
June 12, 2025 at 7:12 AM
@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-...
Check it out here:
www.10xgenomics.com/products/hd-...
Reposted by Koen De Gelas
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
June 11, 2025 at 4:00 PM
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
Reposted by Koen De Gelas
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. 🧵
Wait—wasn’t this a 3′ UMI-based assay for mature mRNA?
Let’s unpack why introns show up—and why they matter. 🧵
June 7, 2025 at 1:45 PM
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. 🧵
Wait—wasn’t this a 3′ UMI-based assay for mature mRNA?
Let’s unpack why introns show up—and why they matter. 🧵
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...
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
June 6, 2025 at 7:00 AM
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...
Full paper: www.nature.com/articles/s41...
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
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
bit.ly
June 5, 2025 at 11:30 AM
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
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
Reposted by Koen De Gelas
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...
May 23, 2025 at 4:30 PM
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...
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
May 25, 2025 at 10:40 AM
New independent single cell benchmarking study by the @fredhutch.bsky.social innovation lab. Check it out! www.biorxiv.org/content/10.1...
Reposted by Koen De Gelas
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
📄 Preprint: doi.org/10.1101/2025...
#spatialbiology #genomics #genetics @lifesciences-ge.bsky.social
May 22, 2025 at 12:03 PM
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
📄 Preprint: doi.org/10.1101/2025...
#spatialbiology #genomics #genetics @lifesciences-ge.bsky.social
Reposted by Koen De Gelas
Only a few days left until our webinar on advancing rare disease research on May 13! 🗓️ Whether you are a researcher, clinician, or student, this webinar will provide valuable knowledge and tools to accelerate your research efforts. Register at bit.ly/42yOfWu
May 9, 2025 at 7:27 AM
Only a few days left until our webinar on advancing rare disease research on May 13! 🗓️ Whether you are a researcher, clinician, or student, this webinar will provide valuable knowledge and tools to accelerate your research efforts. Register at bit.ly/42yOfWu
That will be me presenting! 😀
Join us for a webinar on advancing rare disease research on May 13 at 15:00 CET, where we will discuss the critical importance of advanced genomic solutions in unraveling the mysteries of rare diseases. Registrations are open at bit.ly/42yOfWu
April 30, 2025 at 8:03 AM
That will be me presenting! 😀
Reposted by Koen De Gelas
When high-quality #scRNAseq meets #AI, breakthroughs follow. We’re excited to partner with @arcinstitute.org & Ultima Genomics to grow the Arc Virtual Cell Atlas, an open resource with data from chemical or genetic perturbations, to allow rapid therapeutic target discovery. Read more: bit.ly/42vAd9s
April 28, 2025 at 5:21 PM
When high-quality #scRNAseq meets #AI, breakthroughs follow. We’re excited to partner with @arcinstitute.org & Ultima Genomics to grow the Arc Virtual Cell Atlas, an open resource with data from chemical or genetic perturbations, to allow rapid therapeutic target discovery. Read more: bit.ly/42vAd9s
Heading to Antwerp, Belgium to the VIB conference Revolutionizing Next Generation Sequencing. Looking forward to cutting edge science and technology. Come to the @10xgenomics.bsky.social booth if you want to chat about single cell and spatial biology. #RNGS25
March 19, 2025 at 6:27 AM
Heading to Antwerp, Belgium to the VIB conference Revolutionizing Next Generation Sequencing. Looking forward to cutting edge science and technology. Come to the @10xgenomics.bsky.social booth if you want to chat about single cell and spatial biology. #RNGS25