{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Nares Trakooljul"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-12071"],"description":["This study investigates the effects of exercise and genetic predisposition on the transcriptomic profile of the liver of long-term selected marathon (DUhTP) and non-inbred (DUC) mice. In the exercise group, mice underwent treadmill training for three weeks. For the sedentary control group, mice were kept under minimal physical activities. For the 3-week training program, the mice were running  five days per week (Monday to Friday) starting at age of 49 days after birth (Walz et. al. 2021). All mice used in this experiment were male and sacrificed at day 70 of life for tissue sampling."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA was isolated using TRI reagent (Sigma-Aldrich, Taufkirchen, Germany). DNA traces were removed by DNaseI-treatment (Baseline-Zero DNase; Biozym, Hessisch Oldendorf, Germany), and the RNA was cleaned-up using the RNA Clean&Concentrator-25 Kit (Zymo Research, Freiburg, Germany). RNA quantity was determined using a Qubit fluorometer (ThermoFisher Scientific, Germany), and integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).","Sample Collection - Tissue samples were removed, weighed, snapped frozen in liquid nitrogen, and stored at -70°C.","Library Construction - 1 µg of total RNA with RIN > 8 was used for library preparation using a TruSeq Stranded mRNA Kit with 11 cycles of PCR-amplification according to the manufacture’s recommendation (Illumina).","Sequencing - Multiplexing libraries were sequenced for 2x101bp paired-end reads in high-output mode according to the manufacturer’s recommendation using an Illumina HiSeq 2500 instrument at the Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw FASTQs were quality-checked before and after processing using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Data preprocessing was performed using Trim Galore v.0.6.10. Low quality reads (a mean Q-score < 20) and short reads (<20bp) were removed. Adapter-like sequences at the 3'-end of sequence reads were trimmed. The remaining high quality paired reads were then aligned to the mouse reference genome (Mus_musculus.GRCm39) from Ensembl release 107 using Hisat2-2.2.1. The number of reads uniquely mapped to gene features was extracted to generate gene-count matirx from the aligned bam file using HTSeq."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 2500"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Nares Trakooljul","Andreas Hoeflich","Julia Brenmoehl"],"additional_accession":[]},"is_claimable":false,"name":"RNA-Seq of the liver of mice after 3-week treadmill training versus sedentary control","description":"This study investigates the effects of exercise and genetic predisposition on the transcriptomic profile of the liver of long-term selected marathon (DUhTP) and non-inbred (DUC) mice. In the exercise group, mice underwent treadmill training for three weeks. For the sedentary control group, mice were kept under minimal physical activities. For the 3-week training program, the mice were running  five days per week (Monday to Friday) starting at age of 49 days after birth (Walz et. al. 2021). All mice used in this experiment were male and sacrificed at day 70 of life for tissue sampling.","dates":{"release":"2023-07-01T00:00:00Z","modification":"2026-05-18T13:14:33.446Z","creation":"2022-10-11T00:16:44.8Z"},"accession":"E-MTAB-12071","cross_references":{"ENA":["ERP140191"],"Biostudies":["E-MTAB-12072","E-MTAB-12063","E-MTAB-12065"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}