biostudies-arrayexpressMiguel Gonzalez AceraMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14790Mouse jejunum tissue sections of animals treated with Anti-CD3 antibody for the generation of intestinal inflammation. Samples of the Anti-CD3 treated mice are taken 6 and 24 hours after the administration of the antibody. Samples of animals treated with an isotype antibody are also included, with tissue taken after 24 hours of the administration. Control jejunum sections are included for comparisons.biostudies-arrayexpressSequencing - The clustering of the index-coded samples was performed according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generatedLibrary Construction - Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.Nucleic Acid Extraction - Total RNA was extracted from the samples taken from colons of mice using the peqGOLD total RNA kit (Peqlab/VWR) following the manufacturers' instructions.Sample Collection - Mice were sacrificed and its small intestine was collectedOrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Normalization of the data was performed by DESeq2 using the mean of ratios.Sequence Alignment - Sequence mapping and alignment was performed using STAR v2.7.10bUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAMus musculusJay PatankarMiguel Gonzalez AceraChristoph BeckerfalseAnti-CD3 model of intestinal inflammationMouse jejunum tissue sections of animals treated with Anti-CD3 antibody for the generation of intestinal inflammation. Samples of the Anti-CD3 treated mice are taken 6 and 24 hours after the administration of the antibody. Samples of animals treated with an isotype antibody are also included, with tissue taken after 24 hours of the administration. Control jejunum sections are included for comparisons.2025-05-31T00:00:00Z2025-01-28T22:23:16.755Z2025-01-28T22:23:16.755ZE-MTAB-14790ERP168711EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184