New single cell #perturb-seq dataset added to R2 with Dual #CRISPRi using 20.000+ guide-pairs for HCT116 as well as HEK293T cells.

Check the effect of a guide on any gene directly in R2

R2 nocode open online #datascience platform for biomedical #research

r2platform.com

3100+ citations in PubMed

Coronary artery disease-associated variants regulate vascular smooth muscle cell gene expression - Nature Cardiovascular Research Barbera et al. identify and map genetic variants that alter the characteristics of vascular smooth muscle cells and contribute to the risk of coronary artery disease.

Just in time for #AmericanHeartMonth 🫀

In primary human vascular smooth muscle cells, @metecivelek.bsky.social's lab used state-of-the-art tools, including lentiMPRA & #CRISPRi, to pinpoint functional risk variants for coronary artery disease.

www.nature.com/articles/s44...

#CardioSky 🧪

PrrAB is a Selective Therapeutic Target and Regulator of Respiration in Mycobacterium tuberculosis The essentiality of the PrrAB two-component system (TCS) in Mycobacterium tuberculosis positions it as a promising therapeutic target, prompting investigation into its potential as a universal drug ta...

pubs.acs.org/doi/10.1021/...
Medical scientists have discovered a way to use #CRISPRi to genetically target the system that #Mycobacterium-tuberculosis uses as its heart & lungs, to render it gone.

We’re happy to share our new paper in Genome Biology led by Lingling Wu and Xiang Wu, in collaboration with Xueqiu Lin lab at Fred Hutch. Parallel whole-genome CRISPRi screens in primary human MSCs map distinct regulators of aging processes across organs. #Aging #CRISPRi #Senescence

Jielin Yan (recently graduated 🎉🎉) led the discovery of two enhancers regulating NANOG expression in #hESCs via a #CRISPRi screen. It's part of our larger effort characterizing the functions of enhancers and noncoding variant in development and disease @igvfconsortium.bsky.social

Precise measurement of molecular phenotypes with barcode-based CRISPRi systems - Genome Biology Genome-wide CRISPR-Cas9 screens have untangled regulatory networks driving diverse biological processes. Their success relies on interrogating specific molecular phenotypes and distinguishing key regu...

Nice work from Joseph Lobel on barcode-based #CRISPRi systems!

genomebiology.biomedcentral.com/articles/10....

CRISPRi-Linked Multi-Module Negative Feedback Loops to Address Winner-Take-All Resource Competition Cellular resource limitations create unintended interactions among synthetic gene circuit modules, compromising circuit modularity. This challenge is particularly pronounced in circuits with positive ...

🆕 Another preprint!
CRISPRi-linked multi-module negative feedback loops to combat winner-take-all dynamics from resource competition in gene circuits.
📄 www.biorxiv.org/content/10.1...
#SynBio #CRISPRi #GeneCircuits #ResourceCompetition

Comprehensive interrogation of synthetic lethality in the DNA damage response Nature - Combinatorial CRISPRi screening was used to map genetic interactions in DNA damage response pathways, revealing known and new connections, including the roles of WDR48 and USP1 in...

Thrilled to see this “veritable tour de force” led by John_C_Fielden from Jacob Corn lab out @nature.com, rdcu.be/ehd4E. This @erc.europa.eu funded project uses #CRISPRi to systematically scan 548 DDR genes for synthetic lethal interactions, ~150,000 pairwise combinations!

For biocontainment, we focused on targeting key metabolic genes so C. acnes would only survive if we topically supplement the missing amino acid. Since knocking out genes is still challenging in this skin non-model bacterium, we turned to #CRISPRi to quickly screen auxotrophs.

Source: https://www.biorxiv.org/content/10.1101/2024.11.28.625833v1.full Fig 1 Quantifying knockdown effects in cells from multiple donors at scale. A) Experimental design of a genome-scale CRISPRi screen with single-cell RNA-seq read-out from 34 human iPSC cell lines. B) UMAP of the expression profiles of cells assigned to a donor and targeting guide after correcting for technical covariates, colored by cell line. C) Variance decomposition, displaying relative effects of cell line, genomic background and target gene perturbation on gene expression. D) Overview of the analysis strategy to understand individual trans effects (orange), E) similarity of effects across all genes (green), F) and similarity of perturbation responses across all targets (purple).

A genome-scale single cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines. #PopulationScaleGenomics #CRISPRperturbations #CRISPRi #SingleCell #scRNAseq #GeneRegulation #StemCells @biorxivpreprint.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...