{"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-15480"],"description":["Whole right brain hemispheres of mice with adaptive T-cell transfer colitis and controls to study the impact of gut inflammation on the brain"],"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","Sample Treatment - Naïve CD4+ T cells were isolated from the spleen of C57BL/6J mice using magnetic-based cell separation and subsequently, 1 million CD4+ CD25- cells were injected intraperitoneally into Rag1-/- mice (on C57BL/6J background). Rag1-/- mice injected with 200µL PBS served as controls.","Sample Collection - Three weeks after T cell transfer, mice were sacrificed, transcardially perfused with PBS and right brain hemispheres collected","Nucleic Acid Extraction - RNA isolation was performed using the RNeasy Mini kit (QIAGEN) following the manufacturer’s instructions.","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."],"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":["Heidi Limberger","Jay Patankar","Miguel Gonzalez Acera"],"additional_accession":[]},"is_claimable":false,"name":"Bulk RNA-Sequencing of brain hemispheres of mice with T-cell transfer colitis","description":"Whole right brain hemispheres of mice with adaptive T-cell transfer colitis and controls to study the impact of gut inflammation on the brain","dates":{"release":"2026-01-01T00:00:00Z","modification":"2026-01-02T02:02:39.932Z","creation":"2025-08-12T21:44:36.408Z"},"accession":"E-MTAB-15480","cross_references":{"ENA":["ERP178703"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}