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ENCODE (HG17) region-wide binding of a few antibodies in IFg treated and untreated HeLa cells using nimblegen array

ABSTRACT: Genome-wide location analysis of trimethyl-K4 histone H3 and RNA polymerase II binding in interferon gamma-induced for 30 minutes HeLa cells and uninduced HeLa cells was done using 50mer oligonucletide probes at 38bp intervals tiling over non-repetitive ENCODE regions (HG17, NCBI build 35). There are three replicates for each marker at each state.

ORGANISM(S): Homo sapiens

SUBMITTER: Bing Ren

PROVIDER: E-GEOD-2813 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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ENCODE (HG17) region-wide binding of a few antibodies in IFg treated and untreated HeLa cells using nimblegen array

Project description:Genome-wide location analysis of trimethyl-K4 histone H3 and RNA polymerase II binding in interferon gamma-induced for 30 minutes HeLa cells and uninduced HeLa cells was done using 50mer oligonucletide probes at 38bp intervals tiling over non-repetitive ENCODE regions (HG17, NCBI build 35). Keywords: ChIP-chip

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16MB binding of H3ac, H4ac, STAT1, IRF1 antibodies in IFNg treated and untreated HeLa cells using nimblegen array

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Differential roles of promoters, enhancers, and insulators in cell-type specific gene expression

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Systematic evaluation of variability in simulated ChIP-chip experiments

Project description:The most widely used method for detecting genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first objective analysis of tiling array platforms, amplification procedures, and signal detection algorithms in a simulated ChIP-chip experiment. Mixtures of human genomic DNA and "spike-ins" comprised of nearly 100 human sequences at various concentrations were hybridized to four tiling array platforms by eight independent groups. Blind to the number of spike-ins, their locations, and the range of concentrations, each group made predictions of the spike-in locations. We found that microarray platform choice is not the primary determinant of overall performance. In fact, variation in performance between labs, protocols and algorithms within the same array platform was greater than the variation in performance between array platforms. However, each array platform had unique performance characteristics that varied with tiling resolution and the number of replicates, which have implications for cost versus detection power. Long oligonucleotide arrays were slightly more sensitive at detecting very low enrichment. On all platforms, simple sequence repeats and genome redundancy tended to result in false positives. LM-PCR and WGA, the most popular sample amplification techniques, reproduced relative enrichment levels with high fidelity. Performance among signal detection algorithms was heavily dependent on array platform. The spike-in DNA samples and the data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated. Keywords: ChIP-chip See manuscript for details

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A high-resolution map of active promoters in the human genome

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Ludwig Institute/UCSD ENCODE project June 2007 Release

Project description:The readout of genome information is controlled by transcriptional regulatory elements, but a comprehensive view of the combinatorial control by these DNA sequences, which bind regulatory protein and/or the modified histones in regulating gene transcription, is clearly preliminary. We have developed an experimental strategy for comprehensive determination of such functional elements in human DNA. This strategy involves the application of genome-wide location analysis, also known as ChIP-chip, to a panel of well-characterized regulatory proteins and histones with specific modifications, known to generally associate with transcriptional regulatory elements in vivo. Identification of their genomic binding sites will allow us to determine the sequence features in the human genome that carry out transcriptional regulatory function. We have designed and produced DNA microarrays to represent all the non-repetitive sequences in the 30 million basepair ENCODE regions of the human genome to map various types of transcriptional regulatory elements in three model cell types. We have identified promoters by mapping the genomic sequences associated with RNA polymerase II and the general transcription factor TFIID in cells, enhancer elements by mapping the genomic sequences associated with transcriptional co-activators and enhancer-specific chromatin modifications, and insulators by mapping the genomic sequences associated with the insulator binding protein CTCF. The raw microarray results are released periodically prior to publication. Keywords: ChIP-chip ENCODE ChIP-chip analyses were performed for various transcription factors and chromatin modifications in various cell types. Details to be described in publications. Ren B, Glass CK, Rosenfeld MG, Webster N, Ching KA, Harp L, Ye Z, Stuart RK, Calcar SV, Kim TH, Hawkins RD, Hon G, Barrera LO, Luna R, Wang K

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