biostudies-arrayexpressDamian MoleMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-13049Whole liver tissue RNASeq comparing Kmo wild-type, knockout and hepatocyte-specific knockout micebiostudies-arrayexpressSample Collection - Freshly-harvested liver tissues from mice (n = 3 male mice per group) were snap frozen in liquid nitrogen before storage in a low-temperature freezer at -80°C.Library Construction - After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.Sequencing - The qualified libraries are fed into Illumina sequencers after pooling according to its effective concentration and expected data volume.Nucleic Acid Extraction - Total RNA was isolated from the liver tissue samples using the RNeasy Mini Kit (Qiagen)OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Read counting was performed with featureCounts (Subread version 1.5.2). Differential gene expression analysis between conditions and likelihood ratio tests (to select top genes) were performed with DESeq2 (version 1.20) with R (version 3.5.0). For visualisation purposes, data was transformed using rlog in DESeq2 (log2 transformation and library size-normalisation) and row scaling was applied ((value-mean)/sd)MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq 4000RNA-seq of coding RNAMus musculusDamian MolefalseKynurenine monooxygenase (KMO) knockout mouse liver transcriptomicsWhole liver tissue RNASeq comparing Kmo wild-type, knockout and hepatocyte-specific knockout mice2025-05-31T00:00:00Z2024-05-25T11:00:18.523Z2023-06-07T15:13:11.577ZE-MTAB-13049ERP147998EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184