{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Gong Yu"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16131"],"description":["We performed RNA sequencing on grafts after heart transplantation under three conditions: syngeneic, allogeneic, and allogeneic with anti-CD80/86 antibody treatment."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - The quality of total RNA was assessed using Agilent Bioanalyzer 2200 system (Agilent Technologies, Santa Clara, CA).","Library Construction - Sequencing libraries were generated using NEBNext Ultra™ RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) following the manufacturer’s recommendations.","Sample Collection - Total RNA was isolated from samples prepared from MNCs infiltrating in the allografts using RNeasy Plus Universal Mini Kit (QIAGEN).","Sequencing - The libraries were sequenced on Illumina NovaSeq 6000 (Illumina, San Diego, CA) using a 2 x 150 paired end configuration."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Sequenced reads were filtered to exclude adaptor and low-quality (N > 10% and Q score <= 5) portions. The resulting reads were aligned to the UCSC mouse reference genome (mm10) (http://genome.ucsc.edu/)46 with TopHat47 and assembled with Cufflinks by referring gene structures described in NCBI Reference Sequence (RefSeq) genes.48 For quantification, Fragments Per Kilobase of exon per Million mapped reads (FPKM) was calculated using Cuffquant function in the Cufflinks.48 Immune-related genes were selected as described previously49 and using the Molecular Signature Database (MSigDB)50 on the keywords (immune, lymphocyte and macrophage)."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Gong Yu"],"additional_accession":[]},"is_claimable":false,"name":"Enhancement of suppressive function of Ly49+ CD8+ T cells in allogeneic immunity by CD80/86-CD28 blockade","description":"We performed RNA sequencing on grafts after heart transplantation under three conditions: syngeneic, allogeneic, and allogeneic with anti-CD80/86 antibody treatment.","dates":{"release":"2025-12-31T00:00:00Z","modification":"2025-12-31T02:02:50.74Z","creation":"2025-11-14T13:56:13.348Z"},"accession":"E-MTAB-16131","cross_references":{"ENA":["ERP184452"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}