Evan Macosko

1/8 We learned what kinds of neurons are in the brain with Drop-seq, and where they are located with Slide-seq/tags. But what about their synaptic anatomy?

We developed an imaging-free spatial genomics technology where DNA barcodes diffuse to connect locally. Using UMAP, we reconstructed the physical locations of these barcodes, transforming spatial transcriptomics into purely molecular biology. biorxiv.org/content/10.110…

How do genetic perturbations change cells? How are these effects shaped by cell type and dosage? How do we best extract insight from modern massive perturbation atlases? Im pleased to share a new preprint where we develop a suite of statistical approaches to these Qs (link below)

Hear us talk about Slide-tags!

@marcosanascim This is such fascinating work. LAMP5+ cells are truly intriguing, for more than one reason!

I am thrilled to announce that I will be joining the Department of Genetics at Trinity College Dublin (@tcdgenmicro) in summer 2024! My lab will build and apply new tools to understand the formation and function of microglia states in brain health and disease.

Findings "strongly imply that there is no specific link between maternal mental illness or maternal infection during pregnancy" & neurodevelopmental disabilities (including autism) in offspring cambridge.org/core/journals/… free

A huge congratulations to Jonah Langlieb, Nina Sachdev, @Naeemnadaff, @KarolBalderrama, Mukund Raj, and Chuck Vanderburg. And grateful for the continued collaboration with @insitubiology We hope (and expect!) our atlas helps accelerate many areas of neuroscience research.

We now know the locations of cell types in a full mammalian brain. Our work reveals the brainstem’s absolutely stunning cellular complexity. How and why does it arise? Visit braincelldata.org to plot genes, localize types, and get markers. nature.com/articles/s4158…

Slide-tags unifies the single cell + spatial genomics worlds. It solves three key problems with existing spatial methods: 1) Cell segmentation (the biggest problem) 2) robustness and scalability (well-powered case-control studies now possible) 3) Multiomics (ATAC, RNA, etc)

@GioeleLaManno Congrats Gioele! Very well deserved. So excited by what your lab is doing.

I'm deeply honored and grateful to my incredible team for this achievement. The #SNSF #StartingGrant will transform my dream project into reality. We will study lipids' role in brain development: many discoveries ahead! actu.epfl.ch/news/gioele-la…

The sharing of data is the only way we will make collective progress on hard problems like AD. Our entire dataset and analysis are available at braincelldata.org Vahid Gazestani’s integration of 27 datasets can be easily imported to answer your own scientific questions.

Utilizing rare human brain biopsies we address: 1) Which cell types likely make amyloid? 2) How do microglia respond to amyloid and how does this compare to states in mouse models? 3) What neuronal states precede cell death in AD? Paper out today! cell.com/cell/fulltext/…

Delighted to announce our work developing an approach to understand the function of human microglial states. @MartineTherrie4 and I will guide you through our work, a collaboration with @sasajereb from @macosko and @stevens1lab ! nature.com/articles/s4159…

Congrats @tkam80, Vahid Gazestani and dear collaborators Ville Leinonen and @LabMalm. Amazingly, Vahid integrated our data with most postmortem datasets: braincelldata.org/resource We hope his work provides a common language for discussing cell types and states in human cortex.

How does brain tissue change when amyloid first appears in the brain? In rare surgical biopsies, we find a hyperactive neuronal state preceding loss, and evidence of oligodendrocytes, as well as neurons, producing amyloid. biorxiv.org/content/10.110…

Single-cell or spatial? Our new technology - Slide-tags - allows both in the same experiment, enabling true single-cell multi-modal spatial genomics ➡️ doi.org/10.1101/2023.0…

All single cell assays can now be spatial. Slide tags is simple, reliable single cell with hi-res spatial positioning.  A truly outstanding scientific team: @insitubiology, @andyrusss, @jacksonweir4, Naeem Nadaf. biorxiv.org/content/10.110…

Introducing Slide-tags: our new technology for truly single-cell, multi-modal spatial genomics! Had a blast working alongside @AndyRusss, @Naeemnadaff, @macosko, @insitubiology, and the rest of our team on this project! biorxiv.org/content/10.110… 1/9

Example uses of braincelldata.org: 1) label transfer your sc data to ours. Get cell type assignments and spatial positions. 2) Find genes or cell types enriched in a region. 3) Retrieve the minimal set of genes needed to define a cell type uniquely (ie for FISH).