Thread by @shazanfar

I am extremely excited to share our latest preprint, “Highly multiplexed spatially resolved gene expression profiling of mouse organogenesis”! 🥳 Thread below 👇👇biorxiv.org/cgi/content/sh… 1/n

This represents a massive collaborative effort among several fantastic researchers! Thank you for being such a pleasure to work with @Tim_Lohoff @alsu_troost @omnislip @ebardot @rargelaguet @briscoejames @ReikLab @LongCai_Lab @MarioniLab @LabSrinivas & others not on twitter! 2/n

We’ve generated a high-resolution spatial map of mouse organogenesis using seqFISH with @LongCai_Lab @Caltech which detects hundreds of genes’ expression at the molecular level, along with cell membrane segmentation 3/n

This allows us to quantify the expression of hundreds of genes across single cells within their spatial context which enabled us to perform an integrative analysis with the Mouse Gastrulation Atlas doi.org/10.1038/s41586… 4/n

Meaning that we were able to map and refine cell type information onto our spatial data, and examine these cells’ distribution in space. Using this integration, we were also able to impute the expression profiles of genes not assayed in our targeted seqFISH library. 5/n

We further refined the brain cluster into subgroups corresponding to specific brain regions. We then used diffusion analysis and scHOT testing to look deeper into the developing midbrain-hindbrain boundary and found two distinct axes of development. 6/n

We were able to validate the inferred anterior-posterior axis of the organ progenitor populations spanning the gut tube, previously identified by Kat Hadjantonakis and @dana_peer labs doi.org/10.1038/s41586…, by integrating our spatial data with the single-cell RNA-seq data. 7/n

Additionally, we identified distinct populations of endodermal cells that will give rise to the esophagus and trachea, earlier than expected. These cells separate along the dorsal-ventral axis, a dimension that’s difficult to reconstruct with just scRNA-seq! HCR by @ebardot 8/n

If you’d like to explore the data, have a look at our interactive web app :)
marionilab.cruk.cam.ac.uk/SpatialMouseAt…
9/n

Finally, thanks for reading and a big shout out to everyone involved in this collaboration !! @TheCrick @SCICambridge @BabrahamInst @Cambridge_Uni @CRUK_CI @emblebi @GurdonInstitute @PDN_Cambridge @sangerinstitute @sloan_kettering @Caltech (10/10)

(11/10) It's pretty amazing to see members of the scientific community already using our web app to extract digital in situs of seqFISH (by @Tim_Lohoff and members of @LongCai_Lab) profiled mouse embryos!

https://twitter.com/sonstance95/status/1330101995525562368?s=20

🤩🤩🤩🤩