{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Irina Bochkis"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MEXP-3426"],"description":["Transcriptional profiling of changes in global hepatic gene expression in adult male mice lacking Foxa1 in the liver (Foxa1loxP/loxP;Alfp.Cre)"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Frozen liver tissue was homogenized in Trizol. Following chlorophorm extraction, 1 volume 70% EtOH was added to the aqueous phase, and RNA was extracted using the RNeasy kit (Qiagen). (Parameters: Extracted product = total_RNA, Amplification = none)","Hybridization - Labelled cRNA was hybridized using Agilent hybridization chamber and oven as recommended by the manufacturer  (Parameters: Chamber type = OTHER: Agilent chamber, Quantity of label target used = 825, Mass unit = Nano gram, time = 17, Tiny time unit = hours, Volume = 100, Volume unit = Micro litre, temperature = 65)","Labeling - Five-hundred nanograms of total RNA of each sample were amplified and labeled using the Quick Amp Labeling Kit (Agilent Technologies). (Parameters: Amount of nucleic acid labeled = 500, Amplification = RNA polymerases, Mass unit = Nano gram)"],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","Additional Files","MAGE-TAB Files","Array Designs"],"data_protocol":["Image Adquisition - GenePix quantification (Parameters: Scanning hardware = DNA Microarray Scanner BA [Agilent Technologies], Scanning software = GenePix Pro [Axon Instruments])","Assay Data Transformation - Spot values are darkoffset subtracted, thresholded, and filtered to remove bad spots. The data were normalized by the print tip loess method using the LIMMA (Linear models for microarray data) package in R. For statistical analysis, genes were called differentially expressed using the Significance Analysis of Microarrays (SAM)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"pubmed_abstract":["Gene duplication is a powerful driver of evolution. Newly duplicated genes acquire new roles that are relevant to fitness, or they will be lost over time. A potential path to functional relevance is mutation of the coding sequence leading to the acquisition of novel biochemical properties, as analyzed here for the highly homologous paralogs Foxa1 and Foxa2 transcriptional regulators. We determine by genome-wide location analysis (ChIP-Seq) that, although Foxa1 and Foxa2 share a large fraction of binding sites in the liver, each protein also occupies distinct regulatory elements in vivo. Foxa1-only sites are enriched for p53 binding sites and are frequently found near genes important to cell cycle regulation, while Foxa2-restricted sites show only a limited match to the forkhead consensus a"],"study_type":["transcription profiling by array"],"species":["Mus musculus"],"pubmed_title":["Genome-Wide Location Analysis Reveals Distinct Transcriptional Circuitry by Paralogous Regulators Foxa1 and Foxa2"],"pubmed_authors":["Irina Bochkis","Irina M. Bochkis, Jonathan Schug, Diana Z. Ye, Svitlana Kurinna, Sabrina A. Stratton, Michelle C. Barton, Klaus H. Kaestner"],"additional_accession":[]},"is_claimable":false,"name":"Gene expression profile of Foxa1 in the adult mouse liver","description":"Transcriptional profiling of changes in global hepatic gene expression in adult male mice lacking Foxa1 in the liver (Foxa1loxP/loxP;Alfp.Cre)","dates":{"release":"2012-06-22T00:00:00Z","modification":"2022-11-22T02:13:21.777Z","creation":"2021-10-04T13:11:25Z"},"accession":"E-MEXP-3426","cross_references":{"pubmed":["22737085"],"EFO":["EFO_0002768"],"doi":["doi:10.1371/journal.pgen.1002770"]}}