biostudies-arrayexpressRene KettingCaenorhabditis eleganshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15730This study investigates the role of TOST-1 and the PETISCO complex in regulating histone mRNA stability during Caenorhabditis elegans oogenesis and early embryogenesis. We performed RNA-sequencing analysis on early embryos from tost-1(xf196 ts) temperature-sensitive mutants compared to wild-type controls to understand the molecular basis of TOST-1's essential role in embryonic development and its effects on gene expression timing during the maternal-to-zygotic transition. We examined how temperature affects gene expression, since the developmental phenotype is temperature-dependent: at the permissive temperature (15°C) embryos develop normally, while at the restrictive temperature (25°C) development arrests and embryos die, allowing us to distinguish primary TOST-1 functions from secondary effects of developmental failure.biostudies-arrayexpressGrowth Protocol - C. elegans strains were maintained at 20°C on NGM plates seeded with E. coli OP50. Animals were synchronized by hypochlorite treatment and hatched in M9 buffer for 16 hours. Synchronized L1 larvae were transferred to either 15°C or 25°C incubators and grown to gravid adult stage. Embryos were harvested by hypochlorite treatment when the first laid eggs were observed on plates, approximately 3-4 days post-L1 transfer depending on temperature.Sample Collection - Synchronized gravid adults were subjected to hypochlorite treatment to isolate embryos. Embryos were washed four times with cold M9 buffer and snap-frozen as \"worm balls\" in liquid nitrogen.Library Construction - NGS libraries were prepared using Illumina's Stranded mRNA Prep Ligation Kit with 1000 ng starting material and 10 amplification cycles. ERCC spike-ins (2 μl of 1:100 dilution, Ambion) were added to assess technical variability and optionally assist with library size normalization. Libraries were profiled using DNA 1000 chip on 2100 Bioanalyzer (Agilent) and quantified with Qubit dsDNA HS Assay Kit.Nucleic Acid Extraction - Frozen samples were ground with mortar and pestle, then mixed with five volumes of TRIzol™ LS Reagent (Invitrogen™). RNA was extracted using Direct-zol RNA Microprep kit (Zymo Research™) with additional TURBO DNase treatment (Invitrogen™) to remove genomic DNA. RNA was resuspended in nuclease-free water.Sequencing - All 12 samples were pooled equimolarly and sequenced on NextSeq500 (1×80 cycles plus 10 index cycles).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Raw reads were aligned to C. elegans genome (WBcel235/ce11 assembly) with gene annotation from Ensembl release 104 using STAR (v.2.7) with parameter \"--outFilterMismatchNoverLmax 0.04\". The genome FASTA file and the annotation GTF file were supplemented with data of the added ERCC spike-ins.Data Transformation - Secondary alignments were removed with Samtools (v.1.9) and read counts were summarized on the gene level with Subread featureCounts (v.1.6) using stranded parameter “-s 2” and the above mentioned GTF annotation file.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 500RNA-seq of coding RNACaenorhabditis elegansRene KettingfalseRNA-seq of tost-1(xf196 ts) mutant and wild-type embryos at 15°C and 25°CThis study investigates the role of TOST-1 and the PETISCO complex in regulating histone mRNA stability during Caenorhabditis elegans oogenesis and early embryogenesis. We performed RNA-sequencing analysis on early embryos from tost-1(xf196 ts) temperature-sensitive mutants compared to wild-type controls to understand the molecular basis of TOST-1's essential role in embryonic development and its effects on gene expression timing during the maternal-to-zygotic transition. We examined how temperature affects gene expression, since the developmental phenotype is temperature-dependent: at the permissive temperature (15°C) embryos develop normally, while at the restrictive temperature (25°C) development arrests and embryos die, allowing us to distinguish primary TOST-1 functions from secondary effects of developmental failure.2025-11-11T00:00:00Z2026-05-28T10:25:33.653Z2025-10-15T13:28:26.593ZE-MTAB-15730ERP182221EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184