{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Miguel Gonzalez Acera"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14876"],"description":["The Experiment was performed to understand the changes in expression profile of enteric glia cells in context of intestinal inflammation. Enteric glia are crucial regulators of gastrointestinal motility, however enteric glia alterations in IBD are poorly characterized. Acute T-cell activation rapidly impacts enteric glia activation, and induces cell death pathways, which negatively impacts small intestinal transit. This experiment has been crucial to identify IFNγ- and TNFα -driven necrosis in activated glia cell subsets. In order to sequence pure enteric glia, a mouse strain of Bl6 mice with a Plp1CreERT insert for glial specificity crossed with mice with a flox controlled tdTomato fluorescent protein on the ROSA26 Locus. The mice received a peritoneal injection of an anti-CD3 antibody or its isotype control antibody. At 6 hours, the small intestine was collected and the longitudinal muscle layer with the myenteric plexus stripped off. After enzymatic dissociation and trituration, the enteric glia were FACS sorted and finally the RNA isolated."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - 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 generated","Library 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.","Sample Collection - The mice received a peritoneal injection of an anti-CD3 antibody or its isotype control antibody. At 6 hours, the small intestine was collected and the longitudinal muscle layer with the myenteric plexus stripped off. After enzymatic dissociation and trituration, the enteric glia were FACS sorted and finally the RNA isolated.","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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Normalization of the data was performed by DESeq2 using the mean of ratios.","Sequence Alignment - Sequence mapping and alignment was performed using STAR v2.7.10b"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Marvin Bubeck","Jay Patankar","Miguel Gonzalez Acera"],"additional_accession":[]},"is_claimable":false,"name":"RNA-Seq of FACS sorted Enteric Glia cells from the LMMP after T-cell activation via CD3","description":"The Experiment was performed to understand the changes in expression profile of enteric glia cells in context of intestinal inflammation. Enteric glia are crucial regulators of gastrointestinal motility, however enteric glia alterations in IBD are poorly characterized. Acute T-cell activation rapidly impacts enteric glia activation, and induces cell death pathways, which negatively impacts small intestinal transit. This experiment has been crucial to identify IFNγ- and TNFα -driven necrosis in activated glia cell subsets. In order to sequence pure enteric glia, a mouse strain of Bl6 mice with a Plp1CreERT insert for glial specificity crossed with mice with a flox controlled tdTomato fluorescent protein on the ROSA26 Locus. The mice received a peritoneal injection of an anti-CD3 antibody or its isotype control antibody. At 6 hours, the small intestine was collected and the longitudinal muscle layer with the myenteric plexus stripped off. After enzymatic dissociation and trituration, the enteric glia were FACS sorted and finally the RNA isolated.","dates":{"release":"2025-07-01T00:00:00Z","modification":"2025-02-25T12:24:00.364Z","creation":"2025-02-25T12:24:00.364Z"},"accession":"E-MTAB-14876","cross_references":{"ENA":["ERP169524"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}