{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Saman Rashid"],"organism":["Caenorhabditis elegans"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16084"],"description":["This dataset comprises RNA sequencing and downstream functional analyses of Caenorhabditis elegans models of spinal muscular atrophy (SMA). Samples were collected at the early L4 larval stage from wildtype and smn-1 mutant strains to assess gene expression changes associated with SMA phenotype onset. The submitted data include processed tables for gene ontology enrichment, alternative splicing events, and differential gene expression analyses performed to characterize molecular pathways impacted by smn-1 deficiency. Raw reads for all samples are available in ENA under the provided accession numbers. This dataset supports the findings published in the corresponding manuscript describing SMA pathomechanisms using C. elegans as a model organism."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Libraries were sequenced on an Illumina platform to generate paired end reads. Raw reads in FASTQ format were filtered with fastp to remove reads containing adapters, poly-N sequences, or low-quality bases. Data quality metrics (Q20, Q30, GC content) were calculated for the clean reads, which were used for all downstream analyses. Raw sequencing data for this experiment are archived in the European Nucleotide Archive (ENA) under project PRJEB101991 (runs ERR15810994, ERR15811399, ERR15811400, ERR15811442, ERR15811443, ERR15811444).","Sample Collection - Synchronized populations of C. elegans (wild-type and smn-1 mutants) were cultured on NGM plates seeded with OP50 E. coli and collected at the early L4 stage for RNA extraction.","Nucleic Acid Extraction - Total RNA was isolated from synchronised populations of C. elegans using TRIzol reagent, following standard protocols. Briefly, animals were washed and pelleted by centrifugation, then lysed in TRIzol (ThermoFisher). Samples were subjected to repeated freeze-thaw cycles in liquid nitrogen and a 37°C heating block to ensure complete lysis, followed by phase separation with chloroform (ThermoFisher). The aqueous phase was collected, and RNA was precipitated with isopropanol (ThermoFisher), washed with 75% ethanol, and air-dried before resuspension in nuclease-free water. RNA concentration and purity were determined spectrophotometrically. RNA integrity was assessed by electrophoresis on a 1% agarose-TBE bleach gel, and samples displaying clear 28S, 18S, and 5S rRNA bands with a 28S:18S ratio of ~2:1 were considered high quality.","Library Construction - mRNA was purified using poly-T oligo-attached magnetic beads, fragmented, and used for first- and second-strand cDNA synthesis. After end repair, adaptor ligation, and size selection (150–200 bp), PCR amplification was performed and library quality was verified on the Agilent Bioanalyzer."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw RNA-seq reads were preprocessed by adapter and low-quality base trimming using BBduk. Quality assessment was performed using FastQC and MultiQC. Reads were aligned to a custom C. elegans transcriptome using STAR aligner. Transcript quantification was done using Salmon with the C. elegans reference genome as a decoy.  For normalization, transcript abundances were aggregated at the gene level using tximport. Differential expression analysis was conducted using edgeR in R. Counts were normalized by the trimmed mean of M-values (TMM) method implemented in edgeR to account for library size differences and compositional biases.  Alternative splicing proportions (percent spliced in, PSI) were estimated with SUPPA2, considering events with a minimum total expression threshold. Statistical analyses included generalized linear models with adjustment for multiple testing via the Benjamini-Hochberg method.  This normalization approach reduces technical variability and allows for robust comparison of gene expression and splicing events between smn-1 mutant and wildtype C. elegans."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000","Microcentrifuge, vortex spinner, pipettes, -80C freezer","Zeiss Stereomicroscope, standard lab plasticware","Thermal cycler, Agilent BioAnalyzer 2100"],"study_type":["RNA-seq of coding RNA"],"species":["Caenorhabditis elegans"],"pubmed_authors":["Saman Rashid"],"additional_accession":[]},"is_claimable":false,"name":"RNAseq functional analysis of SMA model in C. elegans at the L4 stage","description":"This dataset comprises RNA sequencing and downstream functional analyses of Caenorhabditis elegans models of spinal muscular atrophy (SMA). Samples were collected at the early L4 larval stage from wildtype and smn-1 mutant strains to assess gene expression changes associated with SMA phenotype onset. The submitted data include processed tables for gene ontology enrichment, alternative splicing events, and differential gene expression analyses performed to characterize molecular pathways impacted by smn-1 deficiency. Raw reads for all samples are available in ENA under the provided accession numbers. This dataset supports the findings published in the corresponding manuscript describing SMA pathomechanisms using C. elegans as a model organism.","dates":{"release":"2025-11-14T00:00:00Z","modification":"2026-05-28T10:25:33.767Z","creation":"2025-11-12T20:03:13.615Z"},"accession":"E-MTAB-16084","cross_references":{"ENA":["ERP184323","ERP183396"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}