biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsSilvere Barontranscription profiling by arrayMus musculusMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-546Lxr-/- mice and WT mice were fed with a western diet and a control diet; Transcriptomic analysis of total RNA samples originated from latero-dorsal prostates was performed as described below between the four conditions: Wild type Mice +/+ on normal diet, Wild type Mice +/+ on western diet, lxr KO Mice-/- on normal diet, lxr KO Mice-/- on western diet. 4 samples will be pooled for each condition: WT +/+ base diet WT +/+ western diet, LXR -/- base diet LXR -/- western diet. Analysis of diet effects: 1. On WT mice: WT Mice +/+ normal diet vs WT Mice +/+ western diet. Wild type base diet RNA pool will be compared to Wild type western diet RNA pool by performing a direct comparison on an Agilent array using the 2-color approach. Dye flips will be prepared for a total of 2 hybridizations. 2. On KO mice: LXR mice -/- base diet vs LXR mice -/- western diet. LXR KO base diet RNA pool will be compared to LXR KO western diet RNA pool by performing a direct comparison on an Agilent array using the 2-color approach. Dye flips will be prepared for a total of 2 hybridizations. Analysis of genotype effects: 1. Under western diet condition: WT +/+ western diet vs LXR -/- western diet. Wild type western diet RNA pool will be compared to LXR KO western diet RNA pool by performing a direct comparison on an Agilent array using the 2-color approach. Dye flips will be prepared for a total of 2 hybridizations. 2. Under base diet condition: WT +/+ base diet vs LXR -/- base diet Wild type base diet RNA pool will be compared to LXR KO base diet RNA pool by performing a direct comparison on an Agilent array using the 2-color approach. Dye flips will be prepared for a total of 2 hybridizations.biostudies-arrayexpressLabeling - RNA Assessment: The quantity of each of the total RNA samples was determined by spectrophotometry and the size distribution was assessed using an Agilent Bioanalyzer. Gene Expression Profiling: Five hundred ng of total RNA was converted into labeled cRNA with nucleotides coupled to a fluorescent dye (either Cy3 or Cy5) using the Low RNA Input Linear Amplification Kit (Agilent Technologies, Palo Alto, CA) following the manufacturers protocol.Nucleic Acid Extraction - Two latero-dorsal lobes of one animal were extracted using Macherey-Nagel RNA extraction kit (740955.250) according manufacturer instructions. RNA samples originated from 4 animals were pooled for each condition.Growth Protocol - Five months old lxr-/- mice and WT mice were fed ad libitum with a western diet and a control diet for five weeks.Chow Diet (Harlan_Teklad-2016S), Western Diet (Harlan_Teklad-TD88051). Mouse strain: 129S6/SvEvTac_Nr1h2tm1Djm/Nr1h3tm1DjmHybridization - Equal amounts of Cy3 and Cy5-labeled cRNA (750 ng) from two different samples were hybridized to Agilent Whole Mouse Genome microarrays. The hybridized array was then washed and scanned and data was extracted from the scanned image using Feature Extraction version 9.5 (Agilent Technologies).MIAME ScoreRaw DataOrganizationAssays and DataAdditional FilesMAGE-TAB FilesArray DesignsJean Marc LobaccaroSilvere BaronAurelien PommierfalseGReD_Prostate_LXRLxr-/- mice and WT mice were fed with a western diet and a control diet; Transcriptomic analysis of total RNA samples originated from latero-dorsal prostates was performed as described below between the four conditions: Wild type Mice +/+ on normal diet, Wild type Mice +/+ on western diet, lxr KO Mice-/- on normal diet, lxr KO Mice-/- on western diet. 4 samples will be pooled for each condition: WT +/+ base diet WT +/+ western diet, LXR -/- base diet LXR -/- western diet. Analysis of diet effects: 1. On WT mice: WT Mice +/+ normal diet vs WT Mice +/+ western diet. Wild type base diet RNA pool will be compared to Wild type western diet RNA pool by performing a direct comparison on an Agilent array using the 2-color approach. Dye flips will be prepared for a total of 2 hybridizations. 2. On KO mice: LXR mice -/- base diet vs LXR mice -/- western diet. LXR KO base diet RNA pool will be compared to LXR KO western diet RNA pool by performing a direct comparison on an Agilent array using the 2-color approach. Dye flips will be prepared for a total of 2 hybridizations. Analysis of genotype effects: 1. Under western diet condition: WT +/+ western diet vs LXR -/- western diet. Wild type western diet RNA pool will be compared to LXR KO western diet RNA pool by performing a direct comparison on an Agilent array using the 2-color approach. Dye flips will be prepared for a total of 2 hybridizations. 2. Under base diet condition: WT +/+ base diet vs LXR -/- base diet Wild type base diet RNA pool will be compared to LXR KO base diet RNA pool by performing a direct comparison on an Agilent array using the 2-color approach. Dye flips will be prepared for a total of 2 hybridizations.2011-03-14T00:00:00Z2022-11-22T12:08:03.824Z2022-03-15T04:26:20.475ZE-MTAB-546EFO_0002768