{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Richard Mott"],"organism":["Mus musculus"],"software":["MicroArraySuite 5.0"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-86"],"description":["Expression profiling of 8 mouse inbred strains on Affymetrix exon specific array"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Labeling - Messenger RNA molecules were amplified using the MessageAmp II-96 Kit (Ambion) according to the manufacturer’s instructions. First strand cDNA was synthesized using 300 ng of total RNA and oligo(dT) primers. In vitro transcription was carried out at 37°C for 14 hours during which biotinylated UTPs (75mM 20 Biotin-16-UTP, Ambion) were used for RNA labeling. Messenger RNA quantity and size was determined in the same way than total RNA using a NanoDrop ND- 1000 Spectrophotometer and an Agilent 2100 Bioanalyser. Size ranged from 250 to 5500 nucleotides with a peak centered at 1000-1500 nucleotides","Sample Processing - All mice were treated identically. They were sacrificed at 6 weeks of age. Tissue was snap-frozen in liquid nitrogen. Whole brains were cut in half sagittally and the left hemisphere soaked into RNAlater-Ice (Ambion) for 20 hours at -20 degree. The hippocampus was dissected for RNA extraction by using TissueLyser and RNeasy Lipid Tissue Kit (Qiagen).","Hybridization - A GeneChip Fluidics Station 450/250 was used to wash and stain the Mouse Exon 1.0 ST Array.","Growth Protocol - Mice were obtained from Harlan UK and housed in open cages  with same-sex litter mates, and fed standard chow.","Nucleic Acid Extraction - Tissue samples  were homogenised using 5 mm stainless steel beads (Qiagen) on a Tissue Lyser (Retsch MM300 Mixer Mill) for 10 minutes at 25 Hertz. Total RNA was then extracted using the RNeasy 96 Universal Tissue Kit (Qiagen) for liver and lung and the RNeasy Lipid Tissue Kit (Qiagen) for hippocampus according to the manufacturer’s instructions. RNA quantity and integrity was assessed using a NanoDrop ND- 1000 Spectrophotometer and an Agilent 2100 Bioanalyser. Total RNA samples with RNA Integrity Number above 9 were used for messenger RNA amplification."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Additional Files","MAGE-TAB Files","Array Designs"],"data_protocol":["Feature Extraction - Title: Affymetrix CEL analysis. Description:"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"pubmed_abstract":["A proportion of the genetic variants underlying complex phenotypes do so through their effects on gene expression, so an important challenge in complex trait analysis is to discover the genetic basis for the variation in transcript abundance. So far, the potential of mapping both quantitative trait loci (QTLs) and expression quantitative trait loci (eQTLs) in rodents has been limited by the low mapping resolution inherent in crosses between inbred strains. We provide a megabase resolution map of thousands of eQTLs in hippocampus, lung, and liver samples from heterogeneous stock (HS) mice in which 843 QTLs have also been mapped at megabase resolution. We exploit dense mouse SNP data to show that artifacts due to allele-specific hybridization occur in approximately 30% of the cis-acting eQTLs and, by comparison with exon expression data, we show that alternative splicing of the 3' end of the genes accounts for <1% of cis-acting eQTLs. Approximately one third of cis-acting eQTLs and one half of trans-acting eQTLs are tissue specific. We have created an important systems biology resource for the genetic analysis of complex traits in a key model organism."],"study_type":["transcription profiling by array"],"species":["Mus musculus"],"pubmed_title":["High resolution mapping of expression QTLs in heterogeneous stock mice in multiple tissues"],"pubmed_authors":["Richard Mott","Huang GJ, Shifman S, Valdar W, Johannesson M, Yalcin B, Taylor MS, Taylor JM, Mott R, Flint J"],"additional_accession":[]},"is_claimable":false,"name":"Transcription profiling of mouse inbred strains (8) on Affymetrix exon specific array","description":"Expression profiling of 8 mouse inbred strains on Affymetrix exon specific array","dates":{"release":"2009-06-04T00:00:00Z","modification":"2022-11-22T19:43:06.69Z","creation":"2022-02-03T14:30:16.685Z"},"accession":"E-MTAB-86","cross_references":{"pubmed":["19376938"],"EFO":["EFO_0002768"],"doi":["19376938"]}}