biostudies-arrayexpressKatrin BohlCaenorhabditis eleganshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-13659The extracellular matrix (ECM) is a pivotal three-dimensional network crucial for tissue organization, cellular communication, and fundamental cellular processes, where collagens are the major chemical entity in amount. Loss of pVHL is associated with the activation of hypoxia-inducible factor (HIF) signaling. Mutation of VHL-1 in the nematode Caenorhabditis elegans has been shown to increase lifespan and stress resistance. Interestingly, considering recent findings on the involvement of collagens in the regulation of lifespan, we also observed these worms to show defects in body morphology in a HIF-1 dependent manner. Here we investigate the impact of vhl-1 (ok161) and hif-1 (ia4) individually and combined over the transcriptome of adult C. elegans worms grown under basal (20°C) conditions, and pay close attention to how genes related to body morphology, such as genes coding for collagens, are regulated.biostudies-arrayexpressSequencing - Sequencing was done by sequencing-by-synthesis with TruSeq v3 chemistry on a HiSeq2500 performed at the Max Planck Genome Center CGC (Cologne, Germany).Sample Collection - Synchronized worms were grown at basal conditions (20°C) and collected at their day 1 adult stage in Trizol (Invitrogen).Library Construction - RNA-Seq libraries were prepared with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs). Capillary electrophoresis (Agilent Bioanalyser and Agilent Tapestation) was used to assess quality and quantity at all steps. Libraries were quantified by fluorimeter, immobilized and processed onto a flow cell with a cBot (Illumina).Nucleic Acid Extraction - Total RNA was extracted using RNeasy Mini spin column (QIAGEN). Concentration and purity of the RNA was measured by NanoDrop. polyA+ mRNA was isolated from total RNA with NEBNext Poly(A) mRNA Magnetics Isolation Module (New England Biolabs).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - The reads were trimmed with Trimmomatic (version 0.36) using default parameters. The trimmed reads were mapped to the WBcel235 Caenorhabditis elegans reference genome with STAR version 2.6.0 using default parameters. Read counts are raw, not normalized.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq 2500RNA-seq of coding RNACaenorhabditis elegansRoman-Ulrich MüllerWillian SalgueiroReza EsmaillieKatrin BohlfalseRNA-seq from hypoxia pathway C. elegans mutants hif-1 (ia4) and vhl-1 (ok161)The extracellular matrix (ECM) is a pivotal three-dimensional network crucial for tissue organization, cellular communication, and fundamental cellular processes, where collagens are the major chemical entity in amount. Loss of pVHL is associated with the activation of hypoxia-inducible factor (HIF) signaling. Mutation of VHL-1 in the nematode Caenorhabditis elegans has been shown to increase lifespan and stress resistance. Interestingly, considering recent findings on the involvement of collagens in the regulation of lifespan, we also observed these worms to show defects in body morphology in a HIF-1 dependent manner. Here we investigate the impact of vhl-1 (ok161) and hif-1 (ia4) individually and combined over the transcriptome of adult C. elegans worms grown under basal (20°C) conditions, and pay close attention to how genes related to body morphology, such as genes coding for collagens, are regulated.2026-06-30T00:00:00Z2026-06-30T01:01:09.046Z2023-12-21T11:09:13.163ZE-MTAB-13659ERP156263EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184