biostudies-arrayexpressDiego Ceacero-HerasMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15441Glucocorticoids are antiinflammatory and immunosuppresive drugs employed in the treatment of inflammatory bowel disease and many other conditions. However, their clinical efficacy is limited due to deleterious effects on the intestinal barrier function. In this experiment, we evaluate rapamycin as a potential candidate to mitigate these deleterious effects on the intestinal barrier while maintaining the antiinflammatory effect of prednisolone, the glucocorticoid used in this experiment.biostudies-arrayexpressLibrary Construction - 'Illumina stranded Total RNA Prep, Ligation with Ribo-Zero Plus e Illumina stranded mRNA Prep, Ligation' protocol was followed.Sample Collection - Distal colon tissue was dissected and washed with cold PBS, then preserved in RNA later (Merck) until RNA extraction.Nucleic Acid Extraction - Total RNA was extracted using RNeasy mini kit (Qiagen), following the manufacturer's instructions.Sequencing - After verifying the concentration, size, and absence of contamination (dimers, primers, etc.), the library pool was denatured and diluted to the required concentration of 0.9 nM. A control library (PhiX) is always introduced with the library to monitor sequencing quality, potential sequencing issues, or unexpected equipment issues. Cluster generation (monoclonal amplification) was then performed on the NovaSeq6000 S2 Flow Cell specified by the user, with 200 cycles and 2 x 100 bp sequencing lengths. Performer:OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Read demultiplexing was then carried out using bcl2fastq2 (Illumina), filtering and trimming was done using Trim Galore (GitHub - FelixKrueger/TrimGalore: A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data). Abundance estimation for transcripts was carried out using Salmon (Salmon provides fast and bias-aware quantification of transcript expression | Nature Methods) aligning against the Ensembl GRCm39 mouse transcriptome (Ensembl 2024 | Nucleic Acids Research | Oxford Academic). Tximeta (DOI: 10.18129/B9.bioc.tximeta) was used for transcript quantification import from Salmon. All data analysis was performed in R programming language and calculation of differentially expressed genes was carried out with the edgeR package (edgeR 4.0: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets | bioRxiv) to carry out quasi likelihood F-tests following a generalized linear model distribution, to account for gene-specific variability and uncertainty in dispersion estimation. Genes were considered differentially expressed when the false discovery rate (FDR) <0.05 and the absolute log2 fold change value < 1 (SI ACABASTE USANDO OTROS CORTES DILO QUE TE ACABÉ ENVIANDO MUCHOS EXCELS). Enrichment analysis was then done with the enrichR package (Gene Set Knowledge Discovery with Enrichr - PubMed) using the Gene Ontology of Biological Processes and the Kyoto Encyclopedia of Genes and Genomes.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAMus musculusDiego Ceacero-HerasFermín Sánchez de MedinaGuillermo Ruiz-HenaresfalseRNA-seq of mouse distal colon treated with prednisolone, rapamycin or both in dextran sodium sulphate (DSS)-induced colitisGlucocorticoids are antiinflammatory and immunosuppresive drugs employed in the treatment of inflammatory bowel disease and many other conditions. However, their clinical efficacy is limited due to deleterious effects on the intestinal barrier function. In this experiment, we evaluate rapamycin as a potential candidate to mitigate these deleterious effects on the intestinal barrier while maintaining the antiinflammatory effect of prednisolone, the glucocorticoid used in this experiment.2025-12-01T00:00:00Z2025-12-01T02:01:52.786Z2025-08-04T10:32:19.178ZE-MTAB-15441ERP177769EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184