Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq

• DOI: 10.1101/2025.02.02.636107
• Publication Date: 2025-02-04T03:10:27Z
• Authors: Hefei Zhang; Xuhang Li; Dongyuan Song; Onur Yukselen; Shivani Nanda; Alper Kucukural; Jingyi Jessica Li; Manuel Garber; Albertha J.M. Wal...
• Keywords: RNA-Seq

The transcriptome provides a highly informative molecular phenotype to connect genotype and is most frequently measured by RNA-sequencing (RNA-seq). Therefore, an ultimate goal perturb every gene measure changes in the transcriptome. However, this remains challenging, especially intact organisms due different experimental computational challenges. Here, we present ‘Worm Perturb-Seq (WPS)’, which high-resolution RNA-seq profiles for hundreds of replicate perturbations at time living animal. WPS introduces multiple advances that combine strengths bulk single cell RNA-seq, further analytical framework, EmpirDE, leverages unique power large datasets. EmpirDE identifies differentially expressed genes (DEGs) using gene-specific empirical null distributions, rather than control conditions alone, thereby systematically removing technical biases improving statistical rigor. We applied 103 Caenhorhabditis elegans nuclear hormone receptors (NHRs) delineate Gene Regulatory Network (GRN) found GRN presents striking ‘pairwise modularity’ where pairs NHRs regulate shared target genes. envision should be useful not only C. , but will broadly applicable other models, including human cells.