New preprint with the Shendure lab @jshendure.bsky.social ! We apply the DNA Typewriter lineage recorder to mouse 3D gastruloids, a powerful model of early mammalian development. Led by Sam Regalado and CX Qiu @cxqiu.bsky.social : www.biorxiv.org/content/10.1... (1/13)

Big thanks to Sam Regalado, @‪cxqiu.bsky.social‬, @jshendure.bsky.social and all co-authors for sharing this journey. Also check out the accompanying preprint applying barcoded monoclonals for lineage recording with @choijunhong.bsky.social. www.biorxiv.org/content/10.1...

Of note, mosaic screens as performed by us or others can still be valuable tools, especially if the extent of heterogeneity is controlled by culturing conditions or quantified up front in absence of perturbations and taken into consideration by sufficient sampling and through biological replicates.

This platform is versatile (EBs are precursors for various organoids), scalable, and opens up new applications, such as studying genetic diseases with reduced penetrance or variable expressivity.

With organoid barcodes we can quantify baseline inter-EB heterogeneity and perturbation-specific changes in cell type composition. We can also apply replicate-based DE analyses, avoiding the high false positive rate caused by inter-EB heterogeneity in standard single cell DE.

Our solution: monoclonal embryoids with an ‘organoid barcode’. This allows us to determine not only the transcriptome and perturbation identity for each cell but also the individual EB of origin - while still growing EBs in a pool, for scalability and shared culture conditions.

Many gRNAs seemed to have significant effects on cell type composition in mosaic EBs, but these were not reproducible across replicates: Stochastic clonal skewing of individual gRNAs in EBs, combined with inter-EB heterogeneity, overwhelms most perturbation effects and reduces statistical power.

Expanding Perturb-seq-like screens to multicellular systems also increases the complexity of confounding effects. We encountered this when we perturbed all TFs in mosaic embryoid bodies (EBs) and develop a scalable solution by barcoding monoclonal individuals. 🧵 www.biorxiv.org/content/10.1...

How is it end of April already? Excited to share that the Kribelbauer Lab is up and running @USC/MCB. Grateful for my first two PhD students @m-finegan.bsky.social @christinagirgis.bsky.social. We are dev scalable, genome-int. tools to study TF & enhancer regulation. Website now live bit.ly/4jo8Tjg

Trying a slightly new model (for us at least) of #openscience. With @ronanchaligne.bsky.social and @karolisk.bsky.social, we pitted 10x Genomics Chromium GEM-X against Illumina PIPseq V head-to-head to understand these two platforms for single-cell genomics. Some thoughts off the bleeding edge: /1

Well said @dereklowe.bsky.social. Academia produces two vital products: (1) knowledge, and (2) human capital that knows how to use it. If we can’t train enough young creative US scientists to fulfill biopharma industry needs…

“I think they're being short-sighted, because fear does that to you.”

Biopharma companies and CEOs are keeping their heads down at their own peril. They should speak up about what’s happening to the NIH and other science agencies before it’s too late.

Silence gives consent. And no one should consent to this.

Nice work, congrats Sud!

Join us for the 6th CRISPR and Beyond Conference on 2-4 April 2025!🧬 A must-attend event for researchers in high-throughput screening and #GeneEditing, exploring emerging technologies and models. #CRISPR25

👉Programme and registration: bit.ly/3Amz34N