Weโre unwrapping a new method today at @mskcancercenter.bsky.social. Led by Sydney Blattman, Nabih Maslah, and @austinv11.com with @danapeer.bsky.social, @ronanchaligne.bsky.social and @10xgenomics.bsky.social, we present GIFT: Genotyping In Fixed Transcriptomes www.biorxiv.org/content/10.6... 1/n
I defended my PhD 10 years ago today. That was the least remarkable thing that happened that day. Sharing something I wrote about it last year. Since then "the horrors persist but so do we." And with dignity.
www.biorxiv.org
Mariko Bennett
Caleb Lareau
We promise that GIFT is something that you're going to want to unwrap soon-- we've been floored by how well this method works. Check out the preprint to learn more! www.biorxiv.org/content/10.6... 8/n
Caleb Lareau
It's cool to see we aren't the only ones that think rationally designed probes + gapfilling is the future. Check out a corroborating workflow from @mgrillo.bsky.social, @lgmartelotto.bsky.social, Anna Nam, and colleagues: bsky.app/profile/mgri... 7/n
The three things you need to know:
1. GIFT uses short DNA probes to enable genotyping anywhere in a transcript and reads out potential mutations with a short 'gapfilling' reaction between adjacent probes. 3/n
I lied-- here's a fourth thing you should know. GIFT is fully loaded and ready to go in your lab.
> The experimental protocol is fully open-sourced.
> We have 3 git repos for probe design, parsing, and downstream analyses
> We've validated it in primary samples and preserved FFPE tissues 6/n
2. GIFT builds on the 10x Genomics Flex kit, enabling a multi-step combinatorial barcoding that scales cell capture for genotype-to-phenotype mapping by ~an order of magnitude. 4/n
3. This design enables genotyping hundreds of loci in individual cells at an accuracy much higher than other workflows for genotyping off of flex. GIFT simply works incredibly well. 5/n
Caleb Lareau
Caleb Lareau
Caleb Lareau
Caleb Lareau
At the risk of duplicating a fairly long primer on the method, I'll share some of the highlights here but refer everyone to this thread on twitter/X 2/n x.com/CalebLareau/...
Caleb Lareau
Really pleased to see this out @natsmb.nature.com: www.nature.com/articles/s41.... MitoPerturb-Seq combines #singlecell #CRISPR screening with whole-cell Multiome, to identify nuclear modifiers of mtDNA dynamics. @mitocamb.bsky.social @mrc-mbu.bsky.social @prudentlab.bsky.social and Stephen Burr
Caleb Lareau
Burr and Auckland et. al develop MitoPerturb-Seq, which combines single-cell screening with multiomics to link nuclear genes to mitochondrial DNA (mtDNA) dynamics. They unveil core regulators of mtDNA...
