Jonathan Weissman's Lab
@JswLab
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Jonathan S. Weissman's lab at the @WhiteheadInst/@MIT. Account run by lab members.
Cambridge, MA
Joined October 2019
RT @LukeKoblan: Excited to announce that this work is now live as a first release article @ScienceMagazine So grateful for this fantatic te….
science.org
Charting the spatiotemporal dynamics of cell fate determination in development and disease is a long-standing objective in biology. Here we present the design, development, and extensive validation...
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RT @GayathriArunaM: Really enjoyed writing this review on the recently expanded landscape of human outer mitochondrial membrane protein bio….
nature.com
Nature Cell Biology - This Review discusses the mechanisms underlying the insertion of α-helical proteins into the mitochondrial outer membrane and highlights the role of convergent evolution...
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RT @inCiChu: Hear it straight from our amazing first author @_annhuang to dive into the X-Atlas/Orion dataset and the FiCS Perturb-seq Plat….
biorxiv.org
The rapid expansion of massively parallel sequencing technologies has enabled the development of foundation models to uncover novel biological findings. While these have the potential to significan...
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1/14.On behalf of the amazing team in @JswLab, we’re excited to share PEtracer ( a prime editing-based evolving lineage recorder compatible with both scRNA-seq and high-resolution imaging readouts in intact tissue. By applying PEtracer in a syngeneic mouse.
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RT @LukeKoblan: 1/14.On behalf of the amazing team in @JswLab, we’re excited to share PEtracer ( a prime editing-ba….
biorxiv.org
Charting the spatiotemporal dynamics of cell fate determination in development and disease is a long-standing objective in biology. Here we present the design, development, and extensive validation...
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Congrats @NadigAjay and @Luke0connor!.
Congrats @NadigAjay on TRADE out now in @NatureGenet: These statistical metrics enable more meaningful comparisons in Perturb-seq atlases. Also, now find the HepG2 and Jurkat Perturb-seq datasets on GEO GSE264667!.
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Congratulations to James Numez and collaborators for their RENDER platform for delivering epigenetic editors using engineered VLPs. RENDER broadly advances our ability to deliver epigenome editors into human cells and will likely find ciritcal uses both in fundamental and.
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RT @ZhuangLab: Delighted to share this preprint from Prof. Rong Fan Lab @RongFan8 and Prof. Sidi Chen lab @sidichen on Spatially Resolved i….
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Our wonderful collaborators on the Perturb-Multi work ( are now here and on the other app, at @ZhuangLab.
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RT @weallen1: In collaboration with Reuben Saunders, @JswLab, and Xiaowei Zhuang, we are very excited to release Perturb-Multi: a platform….
biorxiv.org
Organ function requires coordinated activities of thousands of genes in distinct, spatially organized cell types. Understanding the basis of emergent tissue function requires approaches to dissect...
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We hope that our fixed-cell methods will enable a new era of large-scale in vivo Perturb-seq!.
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The data quality from fixed-cell Perturb-seq is at least as high as that we have seen with RT-based scRNA-seq, and the economics are significantly improved due to the droplet overloading enabled by the probe barcodes from @10xGenomics.
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Fixed-cell Perturb-seq is much easier and less stressful than live cell Perturb-seq—both for the user and for the cells! We love working with samples that can sit in the fridge for days with minimal degradation.
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We then hybridize the fixed cells to custom split probes that directly bind to our sgRNAs, alongside the transcriptome-wide mRNA libraries from @10xGenomics.
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We harvest mosaic mouse tissues by perfusion with formaldehyde, which immediately locks transcriptional phenotypes in place and protects RNA. We then dissociate the fixed tissue and use FACS to select perturbed cells.
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Our fixed-cell Perturb-multi methods enable scRNA-seq and multiplexed imaging on alternate slices from the same genetic mosaic mouse tissues.
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One key component of Perturb-Multi is in vivo Perturb-seq of formaldehyde-fixed tissue, enabled by the Flex reagents from @10xGenomics.
In collaboration with Reuben Saunders, @JswLab, and Xiaowei Zhuang, we are very excited to release Perturb-Multi: a platform for pooled multimodal genetic screens in intact mammalian tissue. Check it out!.
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Perturb-Multi generates rich, multimodal data that can generate fundamentally new insights about the impact of genetic perturbations on tissue function. Check it out!
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