{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"submitter":["Yao D"],"funding":["NHGRI NIH HHS"],"pubmed_abstract":["Pooled CRISPR screens with single-cell RNA-seq readout (Perturb-seq) have emerged as a key technique in functional genomics, but are limited in scale by cost and combinatorial complexity. Here, we reimagine Perturb-seq's design through the lens of algorithms applied to random, low-dimensional observations. We present compressed Perturb-seq, which measures multiple random perturbations per cell or multiple cells per droplet and computationally decompresses these measurements by leveraging the sparse structure of regulatory circuits. Applied to 598 genes in the immune response to bacterial lipopolysaccharide, compressed Perturb-seq achieves the same accuracy as conventional Perturb-seq at 4 to 20-fold reduced cost, with greater power to learn genetic interactions. We identify known and novel"],"journal":["bioRxiv : the preprint server for biology"],"pagination":["2023.01.23.525200"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC9900787"],"repository":["biostudies-literature"],"pubmed_title":["Compressed Perturb-seq: highly efficient screens for regulatory circuits using random composite perturbations."],"pmcid":["PMC9900787"],"funding_grant_id":["R01 HG006399","R01 HG012133","RM1 HG006193"],"pubmed_authors":["Freedman J","Geiger-Schuller K","Gusev A","Binan L","Frangieh CJ","Regev A","Yao D","Bezney J","Cleary B","Eraslan B","Dey K","Simonton B"],"additional_accession":[]},"is_claimable":false,"name":"Compressed Perturb-seq: highly efficient screens for regulatory circuits using random composite perturbations.","description":"Pooled CRISPR screens with single-cell RNA-seq readout (Perturb-seq) have emerged as a key technique in functional genomics, but are limited in scale by cost and combinatorial complexity. Here, we reimagine Perturb-seq's design through the lens of algorithms applied to random, low-dimensional observations. We present compressed Perturb-seq, which measures multiple random perturbations per cell or multiple cells per droplet and computationally decompresses these measurements by leveraging the sparse structure of regulatory circuits. Applied to 598 genes in the immune response to bacterial lipopolysaccharide, compressed Perturb-seq achieves the same accuracy as conventional Perturb-seq at 4 to 20-fold reduced cost, with greater power to learn genetic interactions. We identify known and novel","dates":{"release":"2023-01-01T00:00:00Z","publication":"2023 Jan","modification":"2026-04-08T13:07:11.529Z","creation":"2025-04-05T23:30:10.423Z"},"accession":"S-EPMC9900787","cross_references":{"pubmed":["36747806"],"doi":["10.1101/2023.01.23.525200"]}}