{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Martin Simon"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"organism":["Mus musculus"],"species":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16825"],"description":["This study investigates the correlation of lncRNA Neat1 to liver inflammation and fibrosis. Different diets were applied to wt and Neat1 Knockout Mice:  1. normal diet 2. MCS: methionine-choline-supplemented diet 3. MCD: methionine-choline-deficiend diet The samples represent RNA Seq from liver."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - To isolate total RNA from the mouse liver tissues, 200 µl of TRI Reagent® (Zymo Research Europe GmbH, Freiburg, Germany, catalogue no.: R2053) was dispensed into a 1.5 ml reaction tube. The liver tissues stored at -80°C were then placed on dry ice for the following procedure. A piece weighing approximately 5 mg was cut off with a scalpel and added to the TRI Reagent®. This was homogenised using the Mixy Professional tissue homogeniser (FastGene® Nippon Genetics, Düren, Germany), a further 200 µl of TRI Reagent® was added, the mixture was vortexed for 10 seconds and centrifuged for 1 minute at room temperature at 14.0 x g. The supernatant was transferred to a fresh 1.5 ml reaction tube and the RNA was then isolated using the kit in accordance with the manufacturer’s instructions. The elution volume was 50 µl.","Sequencing - Libraries were dual indexed and sequenced on a Illumina Next Seq 6000S4 lane","Sample Collection - Following the three-week feeding period, the mice were euthanised by CO₂ followed by cardiac incision for serum preparation. The livers were excised, weighed and washed in PBS. The liver lobes were divided and each was flash-frozen in liquid nitrogen in a 1.5 ml reaction tube and stored at -80°C.","Library Construction - Ribisomal RNA was depeleted using the NEB rRNA depeltion Kit and libraries for Illumina were preared using teh NEB NExt Ultra Express RNA Library Kit with 100ng input RNA"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Martin Simon"],"additional_accession":[]},"is_claimable":false,"name":"RNASeq of mice livers with different genotypes","description":"This study investigates the correlation of lncRNA Neat1 to liver inflammation and fibrosis. Different diets were applied to wt and Neat1 Knockout Mice:  1. normal diet 2. MCS: methionine-choline-supplemented diet 3. MCD: methionine-choline-deficiend diet The samples represent RNA Seq from liver.","dates":{"release":"2026-04-07T00:00:00Z","modification":"2026-04-07T17:03:06.634Z","creation":"2026-03-30T13:11:05.812Z"},"accession":"E-MTAB-16825","cross_references":{"ENA":["ERP191552"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"]}}