Computational protocol: Retinoic Acid-Related Orphan Receptor γ (RORγ): A Novel Participant in the Diurnal Regulation of Hepatic Gluconeogenesis and Insulin Sensitivity

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Protocol publication

[…] ChIPed-DNA and input DNA as a control were prepared using RORγ- and RORα-specific antibodies as described previously . ChIP-Seq analysis was performed by the NIH Intramural Sequencing Center and data were analyzed as reported previously . The sequencing reads were obtained from base-calling of Illumina Genome Analyzer. The wiggle-formatted alignment results were visualized on UCSC Genome Browser using mouse mm9 reference genome. SISSRs (Site Identification from Short Sequence Reads) were used for identification of significant RORγ and RORα binding sites (P<0.001) that have enriched reads in each ChIPed-DNA versus input control across the whole genome . The distance from each ROR peak to the nearest transcriptional start sites was determined using custom scripts. De novo consensus motif search within ROR binding sites was performed using MEME. ChIP-Seq data was compared with gene expression data using Kolmogorov-Smirnov (KS) plot. Gene ontology analysis was performed using the NIH Database for Annotation, Visualization, and Integrated Discovery (DAVID) online web-server, and based on PANTHER Biological process definitions. […]

Pipeline specifications

Software tools SISSRs, MEME-ChIP
Databases UCSC Genome Browser
Application ChIP-seq analysis
Organisms Mus musculus, Homo sapiens
Diseases Diabetes Mellitus, Metabolic Diseases
Chemicals Glucose, Tretinoin