biostudies-arrayexpressJonathan PettittCaenorhabditis eleganshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16687The objective of the experiment was to determine the impact of cap-adjacent 2'-O-ribose methylation on steady-state mRNA levels in a background lacking the decapping exonculease EOL-1. We depleted CMTR-1 protein, which is the main enzyme responsible for of cap-adjacent 2'-O-ribose methylation in C. elegans. This was achieved using a strain that is homozygous for an auxin-degron allele of the endogenous cmtr-1 gene in genetic background that constitutively expressed TIR1(F74G) protein (cshIs140 allele derived from HML1012), and also for an eol-1(fe172[E197K]) mutation. The depletion was achieved using the auxin analogue 5-Ph-IAA. Experimental data consists of six replicates, and depletion of CMTR-1 was confirmed by Western blotting.biostudies-arrayexpressNucleic Acid Extraction - 1 ml of Trizol (TRI Reagent, T9424, Sigma Aldrich) was added per 50 µl of worm pellet and samples frozen in liquid N2. Samples were thawed at 37°C and re-frozen four times. They were then vortexed for 30 seconds, left to rest for 30 seconds and the vortex/rest process repeated for a further three times. Phase separation by addition of chloroform and recovery of RNA was done as described by the manufacturer. The aqueous fraction was transferred to a low DNA-binding-tube and diluted 1:1 with 70% ethanol. RNA was purified using PureLink RNA Mini Kit (Thermo Fisher Scientific), using the on-column DNase-treatment option.Sequencing - Six libraries per treatment group (in two batches of triplicates) were sequenced on an Illumina NovaSeq instrument, generating 2x150bp paired-end reads (Novogene UK Ltd).Library Construction - Directional library preparation, with rRNA removal was performed (Novogene UK Ltd).Sample Collection - Worms were washed off NGM plates using M9 and washed 3 times by centrifugation at 749g for 2 min at 4°C.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - The quality of the raw reads was inspected in FASTQC 0.11.9 (Andrews, 2010) and MULTIQC 1.12 (Ewels et al., 2016), and bases with a phred score below 20 were trimmed using TRIMGALORE 0.6.6 (Krueger, 2015). The trimmed reads were then aligned to the C. elegans WB235 reference genome using HISAT2 2.2.0 (Kim et al., 2015). Alignments were processed using SAMTOOLS 1.14 (Li et al., 2009). Gene-level read counts were obtained using FEATURECOUNTS 2.0.2 (Liao et al., 2014), quantifying against exon annotations and assigning fractional counts to all alignment locations of multi-mapping reads. Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Ewels P, Magnusson M, Lundin S, Käller M. 2016. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32:3047–3048. Kim D, Langmead B, Salzberg SL. 2015. HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12:357–360. Krueger F. 2015. Trim Galore!: A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS … Babraham Institute. Li H, Durbin R. 2010. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760. Liao Y, Smyth GK, Shi W. 2014. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923–930.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNACaenorhabditis elegansCap-adjacent 2`-O-ribose methylation of RNA in C. elegans is required for postembryonic growth and germline development in the presence of the decapping exonuclease EOL-1Jonathan PettittEileen Clemens, Sarah Brivio, Mohammed Al-Khafaji, Peter Eijlers, Maheshika Kurukulasuriya, Irmgard U. Haussmann, David MacLeod, Marius Wenzel, Berndt Müller, Matthias Soller and Jonathan PettittfalseRNA-Seq of mRNA derived from fourth larval stage larvae from C. elegans strain PE1328 treated for 16 hours at 20 degrees Celsius with 5-Ph-IAA compared to untreated controlsThe objective of the experiment was to determine the impact of cap-adjacent 2'-O-ribose methylation on steady-state mRNA levels in a background lacking the decapping exonculease EOL-1. We depleted CMTR-1 protein, which is the main enzyme responsible for of cap-adjacent 2'-O-ribose methylation in C. elegans. This was achieved using a strain that is homozygous for an auxin-degron allele of the endogenous cmtr-1 gene in genetic background that constitutively expressed TIR1(F74G) protein (cshIs140 allele derived from HML1012), and also for an eol-1(fe172[E197K]) mutation. The depletion was achieved using the auxin analogue 5-Ph-IAA. Experimental data consists of six replicates, and depletion of CMTR-1 was confirmed by Western blotting.2026-03-05T00:00:00Z2026-03-05T12:01:22.814Z2026-02-26T13:57:17.171ZE-MTAB-16687ERP189674E-MTAB-14816EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184