{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Dag Marcus Eide"],"organism":["Caenorhabditis elegans"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15879"],"description":["This study investigated cellular events and transcriptomic alterations underlying reproductive defects caused by chronic gamma (γ) radiation in Caenorhabditis elegans (C. elegans). Continuous exposure (0, 1 mGy/h [total dose: 0.048 Gy], 10 mGy/h [total dose: 0.48 Gy] and 100 mGy/h; total dose: 4.8 Gy) Total RNA was extracted from 70-h post-L1 males (him-8 strain; ≥ 300 animals per biological replicate, three biological replicates per dose rate) RNAisolation using Direct-zol RNA MicroPrep Kit (Zymo Research, Irvine, CA, USA ) ~30 million 150 bp paired-end reads per sample were generated using half of a Novaseq SP flow cell. Reads were aligned to the C. elegans Ensemble reference genome (WBcel235) using the nf-core/RNA-seq pipeline using the hisat-2 aligner-quantifier."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Type* gDNA Conc. (ng/µl) 21 A260/280 1.79 A260/230 1.79 Volume provided (µl) 95 Total DNA / RNA (µg) 2 Index name (mandatory for libraries, can be left blank for DNA/RNA) N701 Index sequence (mandatory for libraries, can be left blank for DNA/RNA) ATTACTCG Approx no. Reads, Gb or lanes requested  1 Lane Primers, Linkers or RE sites present? † EcoRI digest. All reads start AATTC Comments Pool together with sample 2 in 1 lane","Sample Collection - whole worms from petri dishes, Males were separated from hermaphrodites using 40-µm nylon filters and washed three times with M9 buffer","Nucleic Acid Extraction - Total RNA was extracted from 70-h post-L1 males (him-8 strain; ≥ 300 animals per biological replicate, three biological replicates per condition) subjected to irradiation (0, 1, 10, and 100 mGy/h), using Direct-zol RNA MicroPrep Kit (Zymo Research, Irvine, CA, USA ) according to the manufacturer’s instructions. Males were separated from hermaphrodites using 40-µm nylon filters and washed three times with M9 buffer. The volume was reduced to 150 µL in RNase-free Eppendorf tubes, followed by the addition of 600 µL of Tri Reagent (Zymo Research). Samples were kept on ice before and between homogenization steps using bead beating (⌀ 0.1-0.5 mm) on a FastPrep instrument (10 m/s for 20 seconds, repeated once). Following centrifugation, the supernatant was transferred to new RNase-free tubes, mixed with 750 µL of absolute ethanol, and applied to Zymo-spin IC Columns. On-column DNase I treatment (included in the kit) was performed to remove DNA prior to further purification. RNA concentration (>100 ng/µL), purity (A260/A280 > 1.8; A260/A230 > 2.0), and integrity (RIN > 7) were assessed using Qubit (Thermo Scientific, Waltham, MA, USA), Nanodrop (Thermo Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), respectively.","Library Construction - Library preparation was performed by the Norwegian Sequencing Center (Oslo, Norway) using TruSeqTM stranded RNA-seq paired-end libraries with an average insert size of 350 bp for each biological replicate."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Feature counts from hisat2 from nfcore/RNAseq pipeline"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA"],"species":["Caenorhabditis elegans"],"pubmed_authors":["Hengyi Zhu","Dag Brede","Dag Marcus Eide"],"additional_accession":[]},"is_claimable":false,"name":"RNAseq analysis of dose/dose rate response after gamma Co-60 exposure on C elegans larvae with focus on reproductive effects","description":"This study investigated cellular events and transcriptomic alterations underlying reproductive defects caused by chronic gamma (γ) radiation in Caenorhabditis elegans (C. elegans). Continuous exposure (0, 1 mGy/h [total dose: 0.048 Gy], 10 mGy/h [total dose: 0.48 Gy] and 100 mGy/h; total dose: 4.8 Gy) Total RNA was extracted from 70-h post-L1 males (him-8 strain; ≥ 300 animals per biological replicate, three biological replicates per dose rate) RNAisolation using Direct-zol RNA MicroPrep Kit (Zymo Research, Irvine, CA, USA ) ~30 million 150 bp paired-end reads per sample were generated using half of a Novaseq SP flow cell. Reads were aligned to the C. elegans Ensemble reference genome (WBcel235) using the nf-core/RNA-seq pipeline using the hisat-2 aligner-quantifier.","dates":{"release":"2025-11-30T00:00:00Z","modification":"2026-05-27T17:58:20.603Z","creation":"2025-10-27T20:57:38.578Z"},"accession":"E-MTAB-15879","cross_references":{"ENA":["ERP183148"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}