{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Eugenio López Cortegano"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14914"],"description":["A mutation accumulation (MA) study was performed on C3H/HeNRj mice for 15-19 generations. At the end of the experiment, brain and liver tissue were extracted from 200 mice from 20 MA lines, and RNA was extracted from each tissue sample, with sequencing performed to achieve an expected coverage of over 40 million paired-end reads per sample.  Additionally, control lines derived from cryopreserved embryos were maintained in parallel to the sequenced MA samples, and 100 mice from 10 control lines were sequenced.   See López-Cortegano et al. (in prep) for details."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - The mouse samples sequenced in this study were part of a large mutation accumulation (MA) experiment described in previous studies (see Publications).  All tissue and RNA extractions were made from male mice with similar ages, ranging from 7 to 11 weeks old. Tissue extractions were always carried out at similar times during the day (10am-12am Central European Time) at the facilities of the Max Planck Institute. The whole brain was used for RNA extraction, and liver samples always came from the same liver lobe.","Sequencing - The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina Novaseq, according to effective library concentration and data amount.","Library Construction - After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification","Nucleic Acid Extraction - Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - From the sorted alignment (BAM) files, gene-wise read counts were obtained with the program featureCounts v.2.0.6, including options for quantifying paired-reads (‘-p --countReadPairs’) only when both reads are aligned (‘-B’) and map to the same chromosome and strand (‘-C’).  One expression matrix was obtained per tissue, and read counts were normalised to units of transcripts per million (TPM)","Sequence Alignment - Paired-end reads were aligned against the GRCm39 mouse reference using STAR v2.7.11a with default parameters."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"pubmed_abstract":["New mutations are the source of all genetic variation, including variation affecting quantitative phenotypes. Here, in order to evaluate the impact of mutations on the integrated function of entire tissues, we estimated the mutational variation (V<sub>m</sub>) introduced by new mutations each generation for gene expression. Using deep transcriptome sequencing, we estimated V<sub>m</sub> for brain and liver gene expression in individuals from a mutation accumulation experiment (MA) with the C3H inbred mouse strain. Expression was measured in 200 mice from 40 MA lines maintained for 15-19 generations and in 100 mice from 20 control lines. The control lines allow us to account for environmental variation in gene expression. Based on the difference in the between-line variance component for expression between the MA lines and controls, the median V<sub>m</sub> in the brain was 2.22 × 10<sup>-3</sup>, while in the liver it was markedly lower (V<sub>m</sub> = 0.35 × 10<sup>-3</sup>). A greater proportion of genes also showed V<sub>m</sub> values statistically higher than zero in the brain (29%) than in the liver (7%). These differences could be due to a higher rate of mutation-driven transcriptome evolution in the brain compared to the liver, which we discuss in the context of differences in the mutational target, distribution of mutation effects, cellular complexity, and estimation biases. A differential expression analysis revealed minimal contributions to V<sub>m</sub> from the subset of genes that have significant variation in expression. This indicates that most new mutations exert small effects on gene expression and go undetected in differential expression analyses."],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_title":["Tissue-specific differences of gene expression variance in mutation accumulation lines of mice"],"pubmed_authors":["Eugenio López Cortegano","Eugenio López-Cortegano, Jobran Chebib, Anika Jonas, Sven Künzel, Peter D. Keightley, Diethard Tautz"],"additional_accession":[]},"is_claimable":false,"name":"RNA-Seq Data and Expression Matrices for Brain and Liver from Mice Mutation Accumulation and Control Lines","description":"A mutation accumulation (MA) study was performed on C3H/HeNRj mice for 15-19 generations. At the end of the experiment, brain and liver tissue were extracted from 200 mice from 20 MA lines, and RNA was extracted from each tissue sample, with sequencing performed to achieve an expected coverage of over 40 million paired-end reads per sample.  Additionally, control lines derived from cryopreserved embryos were maintained in parallel to the sequenced MA samples, and 100 mice from 10 control lines were sequenced.   See López-Cortegano et al. (in prep) for details.","dates":{"release":"2025-12-14T00:00:00Z","modification":"2026-04-05T21:18:55.303Z","creation":"2025-03-06T16:58:07.058Z"},"accession":"E-MTAB-14914","cross_references":{"ENA":["ERP170047"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"],"doi":["10.1038/s41437-025-00819-0"]}}