Thread by @fellgernon

🔥off the press! 👀 our @biorxivpreprint on human 🧠brain @LieberInstitute spatial 🌌🔬transcriptomics data 🧬using Visium @10xGenomics🎉#spatialLIBD

🔍spatial.libd.org/spatialLIBD/
👩🏾‍💻github.com/LieberInstitut…
📚research.libd.org/spatialLIBD/
📦github.com/LieberInstitut…

biorxiv.org/content/10.110…

Our study shows 12 samples from 3 human brain DLPFC neuronal layers + white matter with @10xGenomics's Visium platform. Features📜:

* Largest so far
* Harder to cluster than the example mouse data
* Data is all public
* @Bioconductor #rstats📦
* #shiny web app

2/7 #spatialLIBD

* Assessment of known markers
* Identification of layer-specific markers
* smFISH validation✅
* spatial registration of snRNA-seq data
* Layer-enrichment of neurodevelopmental and neuropsychiatric gene sets
* Data-driven layer-enriched clustering in the DLPFC

3/7 #spatialLIBD

This was a great collaboration between @LieberInstitute @jhubiostat @10xGenomics and in particular by @kr_maynard @lmwebr @sudo_BreeB @mattntran linkedin.com/in/nikhil-rao-… @stephaniehicks @martinowk @andrewejaffe

It was a pleasure to be involved in this project!

4/7 #spatialLIBD

And if you want to jump in 🤿and access the data, you can through spatialLIBD::fetch_data() (currently under review at @bioconductor: github.com/Bioconductor/C…) or download the h5, image and loupe files

research.libd.org/spatialLIBD/

5/7 #spatialLIBD #rstats #Bioconductor #OpenScience

+ we'd love to talk to you, hear your feedback, collaborate 🤝and/or hire 👩🏾‍💻👨🏾‍🔬you. Find us at:

March
19 the-scientist.com
26-27

https://twitter.com/VirginiaNeuro/status/1214256625290240000

30 @LIIGH_UNAM

2020 Single Cell Symp.
#BoG2020 @cshlmeetings
@erum2020_conf
#BioC2020 @Bioconductor

6/7 #spatialLIBD

@LIIGH_UNAM @cshlmeetings @erum2020_conf @Bioconductor To close off my 7-layered tweet ;) I wrote a blog post about

"Diving together into the unknown world of spatial transcriptomics"

lcolladotor.github.io/2020/02/29/div…

7/7 #spatialLIBD #stats #scicomm #IntoTheUnknown