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RNA-seq profiles of various developmental stages and systematic nuclear hormone receptor (NHR) gene knockdowns in C. elegans

ABSTRACT: The transcriptome is one of the most informative molecular phenotypes and is most frequently measured by RNA-sequencing (RNA-seq). Recently, Perturb-seq has been developed to measure the transcriptome in single cells upon perturbation of different genes by CRISPR-Cas9. While powerful, Perturb-seq has limited resolution and cannot easily be applied to intact animals. Here, we present ‘Worm Perturb-Seq (WPS)’, which combines whole-animal gene knockdown by RNAi in Caenorhabditis elegans with a large-scale, high-throughput bulk RNA-seq approach that produces high-resolution transcriptome profiles. WPS includes an analytical framework that identifies differentially expressed genes (DEGs) by using gene-specific models with empirical null distributions, rather than using control RNAi alone. Specifically, our approach identifies and corrects inflated P values obtained with standard methods, thus improving statistical rigor. We applied WPS to collect a detailed time course dataset for the animal at various developmental stages, from L2 larve to gravid adult stages. We also applied WPS to 103 C. elegans nuclear hormone receptors (NHRs) and revealed diverse functional modules featuring pairs of NHRs regulating shared target genes. WPS enables large-scale and high-quality transcriptomic analysis of genetic perturbations in an animal and can be implemented not only for RNAi but also for other perturbing conditions such as different bacterial diets, C. elegans strains, etc. WPS may also provide a platform for similar studies in other model organisms and human tissue culture cells.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE255865 | GEO | 2025/02/02

REPOSITORIES: GEO

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