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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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

ABSTRACT: Chromatin immunoprecipitation was performed using antibodies against CTCF and formaldehyde crosslinked chromatin from K562 Chromatin cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions. Keywords: ChIP-chip 3 ChIP-chip Samples

ORGANISM(S): Homo sapiens

SUBMITTER: Lindsey Harp

PROVIDER: E-GEOD-8098 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Histone modifications at human enhancers reflect global cell-type-specific gene expression.

Heintzman Nathaniel D ND Hon Gary C GC Hawkins R David RD Kheradpour Pouya P Stark Alexander A Harp Lindsey F LF Ye Zhen Z Lee Leonard K LK Stuart Rhona K RK Ching Christina W CW Ching Keith A KA Antosiewicz-Bourget Jessica E JE Liu Hui H Zhang Xinmin X Green Roland D RD Lobanenkov Victor V VV Stewart Ron R Thomson James A JA Crawford Gregory E GE Kellis Manolis M Ren Bing B

Nature 20090318 7243

The human body is composed of diverse cell types with distinct functions. Although it is known that lineage specification depends on cell-specific gene expression, which in turn is driven by promoters, enhancers, insulators and other cis-regulatory DNA sequences for each gene, the relative roles of these regulatory elements in this process are not clear. We have previously developed a chromatin-immunoprecipitation-based microarray method (ChIP-chip) to locate promoters, enhancers and insulators ...[more]

PMID: 19295514

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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

2010-05-14 | E-GEOD-10112 | biostudies-arrayexpress

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

2007-06-01 | E-GEOD-7872 | biostudies-arrayexpress

Ludwig Institute/UCSD ENCODE project March 2007 Release

2010-06-12 | E-GEOD-7118 | biostudies-arrayexpress

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

Project description:Analysis of H3ac, H4ac, STAT1 and IRF1 binding in IFNg treated and untreated HeLa cells for 6 hours was done using 50mer oligonucletide probes at 30bp intervals tiling over non-repetitive 16MB gene locus(HG17) Keywords: ChIP-chip three replicates for each marker at each state.

2009-01-14 | E-GEOD-11131 | biostudies-arrayexpress

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

Project description:Chromatin immunoprecipitation was performed using antibodies against CTCF and formaldehyde crosslinked chromatin from K562 Chromatin cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions. Keywords: ChIP-chip

2008-11-01 | GSE8098 | GEO

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). There are three replicates for each marker at each state.

2005-06-15 | E-GEOD-2813 | biostudies-arrayexpress

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

Project description:Our ability to understand the control logic embedded in the human genome is limited by a lack of accurate information of the promoter sequences for most genes. Promoters are a unique class of control sequences, serving as the binding sites for both sequence-specific factors and the general transcription machinery during transcription initiation. In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex throughout the non-repeat sequences of the human genome in primary fibroblast cells. The resulting map defines 10,571 active promoters corresponding to 6,763 known genes and at least 1,199 un-annotated transcriptional units. The map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome. Further examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. Our results provide a global view of the functional relationship among the transcriptional machinery, chromatin structure, and gene expression in human cells. Keywords = GALA Keywords = gene expression Keywords = nimblegen Keywords = promoter profile Keywords = LICR renlab Keywords: other

2010-07-01 | E-GEOD-2672 | biostudies-arrayexpress

ChIP-chip from KG-1 cells with HIV Tat

Project description:HIV-1 Tat can modulate the expression of both HIV and cellular genes. In antigen-presenting cells Tat induces the expression of a subset of interferon-stimulated genes (ISGs) in the absence of interferons (IFNs). We investigated the genome-wide Tat association with cellular promoters in immature dendritic cells (iDC) and in monocyte derived macrophages (MDM). Chromatin immunoprecipitation (ChIP) of Tat together with chromatin profiling by ChIP-on-chip analysis demonstrated that Tat associates with the MAP2K6 and MAP2K3 promoters and mediates its increase, which also affects the induction of some ISGs. comparison of KG-1 cells expressing tTA control vs Tat or mutant TatSF2G48R57A

2013-05-31 | E-GEOD-42191 | biostudies-arrayexpress

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2012-01-19 | E-GEOD-34211 | biostudies-arrayexpress

Genomic discovery of potent chromatin insulators for human gene therapy

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