biostudies-arrayexpressRyo Higuchi-SanabriaCaenorhabditis eleganshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16193The actin cytoskeleton is a highly conserved structural network that supports diverse cellular processes, but its contribution to organismal aging is not well understood. This project investigates how genetic and pharmacological perturbations of actin and actin-binding proteins influence global gene expression and aging phenotypes in Caenorhabditis elegans. Whole-animal RNA interference was used to knock down key actin regulatory genes, including arx-2 (Arp2/3 complex), unc-60 (cofilin), and lev-11 (tropomyosin). Here Bulk RNA sequencing was performed to assess transcriptional responses to actin cytoskeletal disruption using genetic knockdown (RNAi) of actin-binding proteins and actin de/stabilizing molecules. These datasets capture transcriptomic signatures associated with actin dysfunction, aging trajectories, and stress responses, and provide a resource for exploring the molecular links between cytoskeletal integrity and longevity regulation.biostudies-arrayexpressLibrary Construction - Library construction was performed by Novogene using their standard pipeline.Nucleic Acid Extraction - After transfering to 1 mL of TRIzol Reagent, animals are subjected to three freeze/thaw cycles between liquid nitrogen and a 37°C bead bath, with 30 s vortexing between cycles. Following the final thaw, chloroform was added at a 1:5 ratio (chloroform:TRIzol), and RNA was separated by centrifugation in heavy gel phase‐lock tubes (VWR, 10847‐802). The aqueous phase was combined 1:1 with isopropanol, and purification was performed with a QuantaBio Extracta Plus RNA kit (95214) per the manufacturer's instructions.Sample Collection - After bleaching and L1 arrest, worms were grown at 22 °C for 72, 96, or 192 hours to obtain day 1, day 2, and day 6 adult animals, respectively. For each condition, approximately 1,000 worms were collected using M9 buffer and transferred into 1 mL of TRIzol Reagent for RNA extraction.Sequencing - RNA-sequencing was performed by Novogene using their standard pipeline.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Pre-processing to trim low-quality reads and adaptor sequences was performed with Trim Galore v0.6.7-1. Reads were aligned to the WBcel235 genome using STAR‐2.7.3a, and a raw count matrix was generated using Subread v2.0.3. Differential expression was calculated with DESeq2 and sva v3.54.0 was employed to correct for batch effects and non-biological sources of variation.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNACaenorhabditis elegansRyo Higuchi-SanabriafalseForm and function of actin impacts actin health and aging.RNAseqThe actin cytoskeleton is a highly conserved structural network that supports diverse cellular processes, but its contribution to organismal aging is not well understood. This project investigates how genetic and pharmacological perturbations of actin and actin-binding proteins influence global gene expression and aging phenotypes in Caenorhabditis elegans. Whole-animal RNA interference was used to knock down key actin regulatory genes, including arx-2 (Arp2/3 complex), unc-60 (cofilin), and lev-11 (tropomyosin). Here Bulk RNA sequencing was performed to assess transcriptional responses to actin cytoskeletal disruption using genetic knockdown (RNAi) of actin-binding proteins and actin de/stabilizing molecules. These datasets capture transcriptomic signatures associated with actin dysfunction, aging trajectories, and stress responses, and provide a resource for exploring the molecular links between cytoskeletal integrity and longevity regulation.2026-05-11T00:00:00Z2026-05-13T14:10:56.84Z2025-11-19T11:22:02.489ZE-MTAB-16193ERP185320EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184