Tony Zador Profile picture
16 Sep, 11 tweets, 4 min read
Does gene expression predict wiring in the cortex?

Here we introduce a new technique, BARseq2, to answer this question

BARseq2 looks at genes and axon projections at high throughput--thousands of single neurons and many genes per cell in parallel…

This is work by an amazing team: Yu-Chi Sun, Xiaoyin Chen, Stephan Fischer, @starfishlu , and Jesse Gillis

BARseq2 builds on first-generation BARseq (…), which let us look at barcoded axonal projections by in situ DNA sequencing

BARseq2 adds highly multiplexed sequencing of dozens of endogenous genes

shoulders of giants: @MatsNilssonLab @jlee8usa

We hypothesized that cadherin expression was key. So we used BARseq2 to detect cadherin expression and cell type markers in auditory and motor cortex

Laminar patterns of gene expression obtained by BARseq2 were similar to the that seen in the Allen Brain Atlas

The sensitivity of BARseq2 was similar to 10x v3 in this particular experiment, but if we push it we can reach at least 60% of RNAscope

We also determined transcriptomic cell types by detecting additional cell type markers in the motor cortex.

Combining in situ sequencing of barcodes and endogenous genes, we correlated cadherin expression to projections in 1,349 single neurons in auditory and motor cortex.

Gene expression+single neuron axon projection patterns in 1000 neurons, from just a handful of animals!

Our data recapitulated known differences in gene expression and projections between neuronal classes, types, and subtypes.

For example, neurons that project only ipsilaterally were mostly IT4 transcriptomic type (i.e. L6 Car3 type)

How do these cadherins relate to transcriptomic cell types?

To find out, we grouped cadherins into co-expression modules and found that these modules were associated with multiple branches of the transcriptomic taxonomy

Our results suggest that the relationship between gene expression and axonal projections in the cortex is complex

Probably not fully described by the transcriptomic types alone

Maybe the key is to look during development? Or at other genes? Stay tuned...


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More from @TonyZador

19 Mar
What is the Covid-19 endgame? How long are we going to have to live like this?

Right now, it looks like we are going to have to wait at least 12-18 months until we get a vaccine. (1/n)
The devastation to the economy of social distancing practiced at the current level would be mind-boggling, dwarfing pretty much anything we've ever seen. Someone described it as an undergrad dorm discussion for econ majors (2/n)
Maybe some damage could mitigated if we followed the Korean example of aggressive case tracking. Fast and free testing would make that easier. But I think it's still an open question whether this approach will remain effective in Korea...will it come roaring back ? (3/n)
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