biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsSandrine Ellero-Simatostranscription profiling by arrayMus musculusMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16279The aim is to look the effect of dietary fibers (cellulose or inulin) on the hepatic transcriptome of mice fed either a western diet (WD) or a chow diet (CD). C57Bl/6J male mice aged 8 weeks were housed at thermoneutrality (TN, 30°C) and fed a WD or a CD during 17 weeks. CD and WD were supplemented with 9% of dietary fibre which was either pure cellulose (9%, thereafter named “cellulose diet”) or a mixture of cellulose (2.25%) and inulin (6.75%, thereafter named “inulin diet”).biostudies-arrayexpressScaning - Slides were scanned immediately after washing (two wash batches performed as described in \"WashBatch\" characteristics) on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 softwareSample Collection - After 17 weeks of diet exposure, mice were euthanised by cervical dislocation. Liver samples were collected and immediately frozen in liquid nitrogen then stored at -80°C.Nucleic Acid Extraction - Total RNA was extracted using TRI Reagent® (Molecular Research Center, Cincinnati, Ohio, USA). RNAs were quantified using Nanodrop.Hybridization - 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809 enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).Labeling - For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean,Belgium).MIAME ScoreRaw DataOrganizationAssays and DataProcessed DataMAGE-TAB FilesArray DesignsSandrine Ellero-SimatosData Transformation - The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 39 out of 48 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 38874 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 36208 rows each corresponding to a unique ProbeName (provided as data Matrix).falseMicroarray of liver samples from male mice fed a Western-diet or a Chow diet enriched with 9% of cellulose or inulinThe aim is to look the effect of dietary fibers (cellulose or inulin) on the hepatic transcriptome of mice fed either a western diet (WD) or a chow diet (CD). C57Bl/6J male mice aged 8 weeks were housed at thermoneutrality (TN, 30°C) and fed a WD or a CD during 17 weeks. CD and WD were supplemented with 9% of dietary fibre which was either pure cellulose (9%, thereafter named “cellulose diet”) or a mixture of cellulose (2.25%) and inulin (6.75%, thereafter named “inulin diet”).2026-01-01T00:00:00Z2026-05-27T13:32:26.637Z2025-11-25T15:15:37.249ZE-MTAB-16279EFO_0002768EFO_0002944EFO_0003814EFO_0003813EFO_0005518EFO_0003816EFO_0003815