biostudies-arrayexpressDavid Rodriguez CrespoCaenorhabditis eleganshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14523lsy-2 encodes in C. elegans a C2H2 zinc-finger transcription factor involved in the specification of the left-right asymmetry of the ASE neurons (Johnston and Hobert, 2005) and in the maintenance of germ-soma distinction (Lin et al., 2015). RNA for three different biological replicates was isolated from at least 1000 animals of each genotype: wild type and lsy-2(ot64) and then sequence to detect differentially expressed genes in lsy-2 mutant genotype compared to wild type animals.biostudies-arrayexpressLibrary Construction - cDNA libraries were built using the TruSeq stranded mRNA library preparation kit (Illumina Inc.; San Diego CA, USA) by the Next Generation Sequencing (NGS) Platform in Bern (https://www.ngs.unibe.ch/)Nucleic Acid Extraction - Total RNA was extracted with TRIzol Reagent (Invitrogen; Carlsbad CA, USA) and RNA was purified using the PureLink RNA Mini Kit (Invitrogen; Carlsbad IA, USA) according to the manufacturer's instructionsSequencing - RNA sequencing (50 bp paired-end reads) was performed on three biological replicates per sample with the Illumina NovaSeq 6000 Sequencing System and cDNA libraries were multiplexed in a sequencing lane by the Next Generation Sequencing (NGS) Platform in Bern (https://www.ngs.unibe.ch/)Sample Collection - At least 1000 animals from wild-type and lsy-2(ot64) strains were synchronized and collected as young adult hermaphrodites 50 hours post-larval hatching after hypochlorite treatment, at 20°C (Stiernagle, T. 2006).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Raw reads in .fasta format were updated to the Galaxy web platform (https://usegalaxy.eu/). Quality of the reads was confirmed with FastQC, retrieved from http://www.bioinformatics.babram.ac.uk/projects/fastqc/, and the reads were aligned to the C. elegans genome (v. WS235) with Tophat(v. 2.1.1)/Bowtie2(v. 2.2.8) to obtain the .bam files. Read count by gene was obtained by HTSeq-count (Anders et al., 2015) and DE analysis of let-418(s1617) vs. wild type was later performed using DESeq2 package (Love et al., 2014). Read counts were normalized by estimating size factors, and DE was tested against the negative binomial distribution using the Wald test.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNACaenorhabditis elegansChantal WickyDavid Rodriguez CrespofalseRNA-seq of C. elegans young adult hermaphrodites to detect differentially expressed genes in the abscence of lsy-2 activitylsy-2 encodes in C. elegans a C2H2 zinc-finger transcription factor involved in the specification of the left-right asymmetry of the ASE neurons (Johnston and Hobert, 2005) and in the maintenance of germ-soma distinction (Lin et al., 2015). RNA for three different biological replicates was isolated from at least 1000 animals of each genotype: wild type and lsy-2(ot64) and then sequence to detect differentially expressed genes in lsy-2 mutant genotype compared to wild type animals.2025-07-31T00:00:00Z2024-10-09T22:00:23.21Z2024-10-09T22:00:23.21ZE-MTAB-14523ERP164999EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184