Spatial Gut-Microbiome MegaTranscriptomics

Use in situ polyadenylation on #Visium #StereoSeq to enhance host & bacterial RNA recovery (⏫99-fold)

Fresh-frozen🐭GI

Non-coding RNAs enriched to gut wall

Microorganisms enriched at CRC tumor boundary

#NatMicrobiol 2026
www.nature.com/articles/s41...

Fundamental analysis of $VISM (VISIUM TECHNOLOGIES, INC.) based on financial data and reported results.

#VISM #VISIUM

Cynthia S. Cardinault | L. Collado-Torres R/Bioconductor-powered Team Data Science

If any of you are looking for someone to train you on how we organize #RStats / @bioconductor.bsky.social code, #multiome or #Visium analysis using @10xgenomics.bsky.social data, well, now you know whom to contact!

lcolladotor.github.io/authors/cynt...

#OpenToWork

Three representative SRT ERC samples, showing histology, expression of marker genes MBP, PCP4, and SNAP25, and spatial domains

We used #Visium to generate the FIRST spatial transcriptomics dataset of the human #entorhinal cortex. By profiling gene expression across ERC layers with #BayesSpace and #spatialLIBD we uncovered gene expression patterns that could be useful in #Alzheimers research 🧠

Nice #LightningTalk from @maxbeesley.bsky.social as part of #PPCG 2025 meeting

Using @10xgenomics.bsky.social #Visium & #inferCNV to spatially profile clonal heterogeneity & metastasis in #ProstateCancer

#SPACE_Study

@Pinkykotecha.bsky.social
@thineskrishna.bsky.social
@sandyfigiel.bsky.social

This data provides a foundation for future work into molecular changes that occur in the #Habenula in disease 🧠🧬 Keep an eye on @lieberinstitute.bsky.social for future work on the Hb spatially resolved transcriptomics with @10xgenomics.bsky.social tech #Visium and #Xenium 👀 #HabenulaLIBD

Unlock whole transcriptome #spatial analysis with the #Visium HD 3' assay! Take part in our APAC Visium HD 3' Art Gallery. Submit your Visium HD 3' image result and receive: A global spotlight, recognition on custom swag & 50% off your next order. T&Cs apply. https://10xgen.com/1NJ

HAPPENING TOMORROW! You won't want to miss it 🧬

#Xenium #Visium #SpatialOmics #SpatialTranscriptomics

Happening in 1 week - register now! 🧬🔬💻

t.co/xvejAtykmk

#Visium #VisiumHD #Xenium #SpatialTranscriptomics #SpatialBiology #InSituSequencing

10/9/25 9am-4pm see #DukeMGC services at the @10xgenomics.bsky.social #RTP User Group Meeting #10xRTPUGM 🧬

Talks about:
- #GEMX Flex
- Validated #singlecell automation protocols
- #Visium HD larger capture area & poly-A
- #Xenium RNA and protein on 1 slide

pages.10xgenomics.com/ugm-2025-10-...

Join us, Dr. Hwai-Jong Cheng of Academia Sinica, and Dr. Raymond Yip of WEHI for a virtual symposium to explore how #spatial technologies like #Visium and #Xenium are revolutionizing our understanding of clinical and translational research. Register: https://10xgen.com/1PI

Do you want to run @10xgenomics.bsky.social #Visium or another #SpatialTranscriptomics project, but aren't sure how to prep and store your samples? 🧬🧠💻🧪

Check out #DukeMGC Visium project guidelines on our website at dmpi.duke.edu/cores/molecu...

🌟 Thank you to everyone who joined our Visium Spatial Data Analysis Workshop today at Charles Perkins Centre, Sydney!

Participants explored @10xGenomics Visium workflows, data QC, visualisation & downstream analyses, with hands-on support from our team.

#SpatialBiology #Visium #10xGenomics

New collaboration out with #DukeMGC @10xgenomics.bsky.social #Visium data 🧬🔬💻

#SpatialTranscriptomics #Aging #AcutePancreatitis

18- vs 3-mo ♂️🐭+caerulein
#Visium

⏫Inflammation in both Acinar & Stromal cells (even DEGs are similar b/w there 2 compartments)
↔️Major cellular pancreatic fractions

Aging traits of inflamed islets?

#JMolMed 2024
link.springer.com/article/10.1...

Single Cell and Spatial Biology Miltenyi Biotec and 10x Genomics 12:00 to 1:10 p.m. 7/23/25 📅 Date: 7/23/25 📍 Location: Blunt NextGen Precision Health Building - Atkins Family Seminar Room ⏰ Time: 12:00 - 1:10 p.m. Join us for a scientific showcase featuring 10x Genomics and Miltenyi Biotec—...

Don’t miss this lunch and learn #SingleCell & #SpatialBiology with Miltenyi and 10x Genomics @10xgenomics.bsky.social at Mizzou @mizzouid.bsky.social!

📅 July 23, 25
⏰ 12-1:10 PM
📍 Blunt NextGen Atkins Seminar Room

#Visium HD 3' now at Mizzou!
missouri.edu

🥪Lunch provided
forms.gle/JCVUytcF3nyp...

Vispro improves imaging analysis for Visium spatial transcriptomics.#SpatialTranscriptomics #Visium #ImageProcessing #Bioinformatics #Genomics #GenomeBiology 🧬 🖥️
genomebiology.biomedcentral.com/articles/10....

Owkin and UNIL collaborators discuss the MOSAIC study: A conversation with Dr. Elo Madissoon and Dr. Raphael Gottardo - 10x Genomics We interviewed two of the scientists behind the MOSAIC study, a project that will leverage spatial biology and AI to develop targeted therapeutic strategies for cancer.

Read our interview with 2 of the scientists behind MOSAIC, a study that will generate a #Visium #spatialtranscriptomics dataset consisting of 7k+ patient tumor samples to advance therapeutic response modeling and #cancer #drugdiscovery. @owkin.bsky.social @unil.bsky.social

KODAMA goes spatial.
doi.org/10.1101/2025...
#spatialtranscriptomics #visium #visiumhd #seurat #giotto

Join @10xgenomics.bsky.social's webinar Thurs June 4 to explore the capabilities of the new #Visium HD 3’ assay.
Registration 🔗: 10xgen.com/1Nd

Check out this comprehensive evaluation of how sample handling can increase data quality with the #Visium spatial platform! And specifically, how CytAssist-enabled transcript localization and microfluidic control make a difference. Read the paper here: bit.ly/3Eyjt8e

#SpatialTranscriptomics #Visium (n=2) human #UterineLeiomyoma
+snRNAseq

Tumor vs Pseudocapsule vs Myometrium

5 ACTA2+ACTG2+ #SmoothMuscleCell states
3 PDGFRB+NOTCH3+ #Pericyte states
Love to see more analysis...🤓

ERβ⏫in angiogenic #EndothelialCell

#IntJBiolSci 2023
www.ijbs.com/v19p2515.htm

Spatial Mechano-Transcriptomics mouse #BoneFracture #Mechanomics

#Visium #SpatialTranscriptomics
+Bone mechanical mapping◀️Axial compressive strain simulation◀️µCT + finite element modeling

High strain >1000 με➡️⏫Bone anabolism + Osteoclastogenesis

#SciAdv 2025
www.science.org/doi/10.1126/...

📝 Note: These analyses were done on Visium data courtesy of 10x Genomics, but the approaches apply to other grid-based spatial technologies, like Visium HD.

#SpatialTranscriptomics #SingleCell #Bioinformatics #Visium #10xGenomics #CancerResearch #SpatialOmics #SpatialBiology

APOBEC3B is not detected in #Visium or #scRNAseq but highly expressed in #Xenium, despite these being serial sections from the same sample. Our tool predicted APOBEC3B probes to exhibit off-target binding to APOBEC3F, APOBEC3A, APOBEC3D. Our comparative analysis substantiates this prediction (9/n)

We further observe that the gene expression pattern of the aggregate of TUBB2B + TUBB2A in #Visium and #scRNAseq is visually more similar to the pattern of TUBB2B alone in #Xenium, consistent with the prediction that Xenium TUBB2B probes exhibit off-target binding to TUBB2A (7/n)

High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis - Nature Communications The integration of single-cell and spatial data can provide a more comprehensive picture of the network of cells within the tumour microenvironment. Here the authors use a combination of single-cell a...

To substantiate our predictions, we leveraged a previously published #Xenium breast cancer dataset generated using this gene panel (www.nature.com/articles/s41...) + compared gene expression profiles to orthogonal #spatialomics and #singlecell transcriptomic profiles from #Visium and #scRNAseq (4/n)

Wrapping up our #10xOmix Melbourne lightning talks, Natalie Charitakis (MCRI) is discussed, "Multi-Slice analysis Cardiac rhabdomyoma data generated with #Visium to reveal novel signatures of the benign tumour".

Julia Cowen (Associate Director, @10xgenomics.bsky.social) presenting at #10xOmiX Melbourne this morning discussing how you can discover spatial insights with #Visium HD and #Xenium.

Teaching omics methods to LCG-UNAM students | L. Collado-Torres Notes from a second semester introductory class to the world of omics research techniques at LCG-UNAM. That is, my undergrad alma mater. Thank you for the invitation! Valentina Arias Ojeda is as teach...

New blog post: "Teaching #omics #methods to #LCG-UNAM students"

Thanks for inviting me @vaalarias.bsky.social and Dr Constance Auvynet ^_^

Blog post is available in both English and Spanish 🇲🇽

#genomics #scRNAseq #Visium #spatialomics @10xgenomics.bsky.social

lcolladotor.github.io/2025/03/07/t...