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GenomicsHighly efficient genomic enrichment of human exonic sequences through short-fragment libraries
Microarray-based enrichment of selected genomic loci is a powerful method for genome complexity reduction. Since the vast majority of exons in vertebrate genomes are smaller than 150 nt, we have explored the use of short fragment libraries (85-110bp) to achieve higher enrichment specificity by reduc...
ORGANISM(S): Homo sapiens 
2010-02-01 | E-GEOD-18542 | biostudies-arrayexpress
GenomicsInflammatory bowel disease risk loci overlap with DNA regulatory regions in immune cells and intestinal epithelium
Background & Aims: The contribution of genetics to the pathogenesis of inflammatory bowel disease (IBD) has been established by twin studies, targeted sequencing and genome-wide association studies (GWASs). This has yielded a plethora of risk loci with an aim to identify causal variants. Research on...
ORGANISM(S): Homo sapiens 
2013-12-06 | E-GEOD-51425 | biostudies-arrayexpress
GenomicsDouble fragmentation ChIP-seq provides single nucleotide resolution Tcf4 binding characteristics
ChIP-seq has become the method of choice for studying functional DNA-protein interactions on a genome wide scale. The method is based on co-immunoprecipitation of DNA binding proteins with formaldehyde cross-linked DNA, followed by deep sequencing of immunoprecipitated chromatin fragments, allowing ...
ORGANISM(S): Homo sapiens 
2010-11-01 | E-GEOD-18481 | biostudies-arrayexpress
GenomicsComparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq
The goal of the ChIP-seq study was to investigate the distribution of the TATA-binding protein (TBP) across the human genome. TBP is the DNA-binding subunit of the basal transcription factor TFIID for RNA polymerase II (pol II) and it also participates in other complexes for the other RNA polymerase...
ORGANISM(S): Homo sapiens 
2010-03-02 | E-GEOD-17937 | biostudies-arrayexpress
GenomicsNext Gen(etics): targeted genome enrichment and next-generation sequencing enhances phenotype-driven forward genetics and gene-driven reverse genetics
Targeted genomic enrichment followed by next-generation sequencing dramatically increased the efficiency of mutation discovery in human genomes. Here we demonstrate that these techniques also revolutionize traditional genetic approaches in model systems. We developed a two-step protocol utilizing a ...
ORGANISM(S): Rattus norvegicus 
2010-09-12 | E-GEOD-22024 | biostudies-arrayexpress
GenomicsE2F7 represses a transcriptional network of oscillating cell cycle genes to control S-phase progression.
E2F transcription factors are known to be important for timely activation of G1/S and G2/M genes required for cell cycle progression, but transcriptional mechanisms for deactivation of cell cycle regulated genes are unknown. Here, we show that E2F7 is highly expressed during mid to late S-phase, occ...
ORGANISM(S): Homo sapiens 
2012-01-04 | E-GEOD-32673 | biostudies-arrayexpress
TranscriptomicsDeciphering the Wnt-dependent gene signature in colorectal cancer cells
Microarray-based gene expression data were generated from RNA from Ls174T colorectal carcinoma cell lines in which Wnt-dependent transcriptional activity can be abrogated by inducible overexpression of a dominant-negative form of Tcf4 or siRNA against M-NM-2-catenin. shRNA against M-NM-2-catenin, or...
ORGANISM(S): Homo sapiens 
2011-11-29 | E-GEOD-18560 | biostudies-arrayexpress
GenomicsIntegrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes
Routine methods for assaying steady-state mRNA levels such as RNA-seq and micro-arrays are commonly used as readouts to study the role of transcription factors (TFs) in gene expression regulation. However, cellular RNA levels do not solely depend on activity of TFs and subsequent transcription by RN...
ORGANISM(S): Homo sapiens 
2012-03-09 | E-GEOD-36349 | biostudies-arrayexpress
TranscriptomicsAdult stem cells in the small intestine are intrinsically programmed with their location-specific function
Differentiation and specialisation of epithelial cells in the small intestine is regulated in two ways. First, there is differentiation along the crypt-villus axis of the intestinal stem cells into absorptive enterocytes, Paneth, goblet, tuft, enteroendocrine or M-cells, which is mainly regulated by...
ORGANISM(S): Mus musculus 
2014-01-07 | E-GEOD-53297 | biostudies-arrayexpress
GenomicsGene expression profiling and TF occupancy upon treatment with the FXR agonist obeticholic acid
The farnesoid X receptor (FXR) is a nuclear receptor activated by bile acids and regulates bile acid metabolism, glucose and cholesterol homeostasis. From mouse studies we know that the novel FXR agonist obeticholic acid (OCA) regulates expression of many genes in the liver, but there is currently n...
ORGANISM(S): Mus musculus 
2016-01-27 | E-GEOD-73624 | biostudies-arrayexpress
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