biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsSarah Janssentranscription profiling by arrayMus musculusMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-GEOD-49974This SuperSeries is composed of the SubSeries listed below. Refer to individual Seriesbiostudies-arrayexpressLabeling - aRNA samples were labeled with a Cy5 fluorescent probe (Cy5 mono-reactive dye pack, GE Healthcare UK, Little Chalfont, Buckinghamshire, UK). In short, aRNA was coupled to Cy5 (dissolved in DMSO) in 0.5 M NaHCO3 (pH 9.0) for one hour. Free dyes were quenched by the addition of 4 M hydroxylamine and removed by filtration over a Chroma Spin-30 column (DEPC-H20 Columns, Clontech Laboratories) with glycogen as a carrier.Hybridization - Labeled human CPE RNA and labeled human common reference sample were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentialNucleic Acid Extraction - Total RNA was isolated using RNeasy Micro Kit (Qiagen Benelux, Venlo, The Netherlands). Subsequently, the mRNA component was amplified with Amino Allyl MessageAmp II aRNA Amplification kit (#1753, Ambion Applied Biosystems Europe B.V.).Hybridization - Labeled mouse CPE RNA and labeled mouse common reference sample were applied to microarrays slides enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentialSample Treatment - With laser dissection microscopy, the CPE cells were specifically cut out from cryosections of the choroid plexus (10um) mounted on PEN-membrane slidesSample Treatment - With laser dissection microscopy, the CPE cells were specifically cut out from cryosections of the whole brain (20 um) mounted on PEN-membrane slidesScaning - Scanned on an Agilent scanner, protocol GE2-v4_95_Feb07 for mouse dataScaning - Scanned on an Agilent scanner, protocol GE2-v5_95_Fec07MIAME ScoreRaw DataOrganizationAssays and DataProcessed DataMAGE-TAB FilesArray DesignsSarah JanssenData Transformation - Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and linear loweless dye normalization. This resulted amongst others in normalized log ratios (test/reference) data that can be find in the Agilent Feature Extraction files. Further data processing was done in R (version 2.14.0 for Windows, R Development Core Team, 2009), with package Limma. We read in the raw data (RG <-read.maimage). Next, we normalized the data within arrays (method 'loess', resulating in MA) and between arrays (method aquantile). In the matrix table, we listed these normalized red channels of each mouse CPE sample (log2). ID_REF = VALUE = normalized red channels (log2)Data Transformation - Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and linear loweless dye normalization. This resulted amongst others in normalized log ratios (test/reference) data that can be find in the Agilent Feature Extraction files. Further data processing was done in R (version 2.14.0 for Windows, R Development Core Team, 2009), with package Limma. We read in the raw data (RG <-read.maimage). Next, we normalized within arrays (method 'loess', resulating in MA) and between arrays (method aquantile). In the matrix table, we listed these normalized red channels of each human CPE sample (log2). ID_REF = VALUE = normalized red channels (log2)falseGene expression of the choroid plexus epithelium (CPE)This SuperSeries is composed of the SubSeries listed below. Refer to individual Series2013-09-27T00:00:00Z2023-09-06T04:56:27.367Z2022-03-07T00:35:50.779ZE-GEOD-49974GSE49974EFO_0002768