Excited to share the second piece of my PhD work! Our paper on generating 2D and 3D spatial transcriptomic maps of whole mouse embryos during early organogenesis with @adrianobolondi @Luyi_T is out in @NatureGenet 🐭🧬 @MPI_MolGen @broadinstitute.

Check out this amazing work from @PGuckelberger @jengreitz , answering an important question on how 3D contacts tune enhancer effects on gene expression. Congratulations to the entire team.

First one out from @Luyi_T lab in @naturemethods congratulations to all authors. Happy to have contributed.

In the multi-donor brain chimeroids, we also show that the different donor lines are spatially distributed, profiled with Curioseeker @curiobio . Excited to have contributed to this tremendous work led by @BolanosAnton @IreneFaravelli @ArlottaLab. Congratulations to all authors.

A fantastic and systematic study from @Maxistoe @bulutkarslioglu ! Kudos to @Maxistoe for his hardwork, dedication and success. Happy to have contributed. Congratulations to all the authors @MPI_MolGen.

I am excited to share the final version of this work published today in @NatureCellBio. A great collaboration with Liat,@EddaGSchulz and the entire team @MPI_MolGen.

Register now to attend the webinar on the 1st of November. We’ll discuss our efforts in reconstructing 3D spatial maps and using it to understand tissue patterning in the embryo.

Join us on the 1st of November to learn about our efforts in reconstructing 3D spatial transcriptomic maps of whole mouse embryos.

Check out this really exciting work from @ArlottaLab @BolanosAnton @Irene_Faravelli and team. The multi-donor chimeroid with various genetic backgrounds is a great platform for scalable testing of genetic susceptibility to neurotoxic triggers.

RT @HCRimaging: This week’s #FluorescenceFriday user is Abhishek Sampath Kumar! @AbhiSampKumar applied #HCRimaging to confirm the expressio….

Check out how sc3D can be used to reconstruct, visualize and analyze 3D spatial gene expression patterns from other datasets (such as Stereo-seq) @GuignardLab @TheBgiGroup.

RT @HSCRB: New research in @NatureGenet presents an experimental and computational framework for the spatiotemporal investigation of whole….

RT @adrianobolondi: 🚨Paper alert🚨 With @AbhiSampKumar, @Luyi_T & @GuignardLab we built a 3D spatial transcriptomic atlas of mouse embryos t….

RT @GuignardLab: 📢📢Always wanted to look at all expressed genes in whole E8.5/9.0 mouse embryos, at near single cell resolution while keepi….

Big shout out to @AAragonesH , Bob Stickels, Evan, @helenekretzmer , Maria, Lars, Leah, Gabriel, @ElkabetzYechiel ,@macosko ,@insitubiology ,@GuignardLab , and Alex for their remarkable contributions to this work.Your collaboration has been instrumental in this endeavor. (11/11).

Our comprehensive spatial transcriptomic maps, along with the computational tools developed, provide valuable resources for studying mammalian development. This framework opens new avenues for conducting "molecular spatial phenotyping" across a wide range of perturbations.(10/11).

We find that 'ectopic tubes' display a conflicting molecular identity (neural and mesodermal) and loss of complete DV patterning. This highlights an uncoupling between morphogenetic outcomes and transcriptional state. #NotInTheGenes (9/11).

Slide-seq allows us to investigate molecular features of developmental phenotypes at the spatial level. We revisited the classical Tbx6 mutant, which generate ‘ectopic’ tubes and fail to develop somites. (8/11).

Probing localized patterns along the DV neural tube axis, we unravel ~40 genes with distinct spatial gene expression localization. These findings extend the putative regulatory networks shaping neural tube formation and functional diversification. (7/11).

Exploring the relationship between distance and transcriptional divergence, we found transcriptomic changes are not always proportional to cell-cell distances, revealing tissue-specific dynamics within the trunk, such as that of the neural tube dorsoventral patterning. (6/11).

Leveraging the power of our high-resolution atlas, we probed regionalized gene expression patterns in embryonic tissues in an unbiased manner. These patterns illuminate the formation of future anatomical or functional domains, like brain boundaries and the developing eye. (5/11).