(A) Identification of MYCN binding upstream of NME2. The scale across the top of the panel indicates the base pair position on chromosome 17. Fluorescent intensity of probes from experiments using 2 independent MYCN antibodies around the NME2 promoter are expressed as log2 ratios (green bars) and high confidence MYCN peaks (red bars) as identified by the NimbleScan peak finding algorithm. Position of the NME2 transcript and the region tiled on the array are indicated by the bottom two panels. (B) Total number of MYCN peaks identified across neuroblastoma cell lines. Venn diagrams (i–v) display the number of MYCN peaks which is shared and unique to each cell line. Statistical significance of overlap for all comparisons was determined to be statistically significant (P<0.001) by Fisher's Exact Test.

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Mining ChIP-chip

Andrew D. Smith, Pavel Sumazin, Debopriya Das et al. · 2005

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and ChIP-chip

Hao Sun, Saranyan K. Palaniswamy, Twyla T. Pohar et al. · 2005

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CHIP Magazine, CHIP

Rice Digital Scholarship Archive (Rice University) · 2011

This image contains 8 people; 5 male(s); 3 female(s); 8 Asian; The origin of the image is Domestic. Watermark Unknown.

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Epigenetic Analysis: ChIP-chip and ChIP-seq

Matteo Pellegrini, Roberto Ferrari · Methods in molecular biology · 2011

The access of transcription factors and the replication machinery to DNA is regulated by the epigenetic state of chromatin. In eukaryotes, this complex layer of regulatory processes includes the direct methylation of DNA, as well as covalent modifications to histones. Using next-generation sequencers, it is now possible to obtain profiles of epigenetic modifications across a genome using chromatin immunoprecipitation followed by sequencing (ChIP-seq). This technique permits the detection of the binding of proteins to specific regions of the genome with high resolution. It can be used to determine the target sequences of transcription factors, as well as the positions of histones with specific modification of their N-terminal tails. Antibodies that selectively bind methylated DNA may also be used to determine the position of methylated cytosines. Here, we present a data analysis pipeline for processing ChIP-seq data, and discuss the limitations and idiosyncrasies of these approaches.

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Confirmation of ChIP-chip by ChIP-Qpcr.

Adnane Sellam (141829), Faiza Tebbji (141832), Malcolm Whiteway (30367) et al. · Figshare · 2015

In vivo occupancy of Cwt1p at ten different intergenic regions. Immunoprecipitated DNA was subjected to qPCR to validate Cwt1p binding at 100–200 bp regions surrounding the probes showing a significant binding ratio. SDs were based on data from two independent experiments.

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Chip-to-Chip and On-Chip Communications

Nossek, Josef A., Russer, Peter, Noll, Tobias G. et al. · RWTH Publications (RWTH Aachen) · 2012

Cited by 9Open access

Jahresarchiv ... Chip HD-Welt, Chip, Chip Foto Video, Chip Test & Kauf

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ChIP-chip enriched genes.

Juliane Bock (105292), Liliana H. Mochmann (105294), Cornelia Schlee (105296) et al. · Figshare · 2015

Displayed are 8 ChIP-chip samples with the ERG mRNA expression measured by quantitative real-time PCR as well as the number of significantly enriched single genes, identified by ChIP-chip using BRB Array Tools (fold enrichment >1.25, p<0.05), for primary AML samples (AML A through AML E), for T-ALL (T-ALL), a normal bone marrow sample (nBM) and the cell line HL60.

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Chip-to-Chip Interface

Robert Drost, Bidirectional Single-ended, High Speed et al. · 2002

the degree of Doctor of Philosophy. Advances in integrated circuit technologies permit faster clocking speed and increased logic density in chips. However, advances in chip packaging technologies have not kept pace; hence the number of input/output pins and input/output bandwidth per chip has increased less rapidly. The resulting disparity creates the need for more bandwidth per pin. Single-ended signalling and simultaneous bidirectional signalling methods may each increase the bandwidth per pin by a factor of two. However, using these signalling methods poses challenges in compensating for additional noise sources and reduced noise rejection ratios. This work presents the architecture, circuit techniques, and test results for a single-ended simultaneously bidirectional interface capable of a total throughput of 8 Gigabits per second per pin. The interface addresses the noise reduction challenges by utilizing a pseudo-differential reference with noise immunity approaching that of a fully differential reference. Furthermore, noise generation is reduced by on-chip termination, and low-skew near-end outgoing signal echo cancellation. A test chip in a 0.35 micron digital CMOS technology uses these techniques for an eight bit wide single-ended voltage-mode simultaneous bidirectional interface and achieves a performance of 8 Gigabit per second per pin.

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Chromatin Immunoprecipitation for ChIP-chip and ChIP-seq

Sebastian Schulz, Susanne Häußler · Methods in molecular biology · 2014

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Summary of ChIP-chip and classical ChIP experiments.

Michal Krawczyk (24804), Queralt Seguín-Estévez (24806), Elisa Leimgruber (24805) et al. · Figshare · 2015

1Results of independent CIITA-ChIP-chip experiments performed with NimbleGen promoter arrays: + signs indicate the presence of a peak in the signal ratios; the number of + signs refers to the quality of the peaks; +++ indicates strong signals (log2 ratio > 2) at four or more adjacent oligonucleotides or weaker signals at more than four adjacent oligonnucleotides; ++ indicates strong signals at three adjacent oligonucleotides or weaker signals at four adjacent oligonucleotides; + indicates strong signals at two adjacent oligonucleotides or weaker signals at three adjacent oligonucleotides.2Results of classical CIITA-ChIP experiments: positive, confirmed binding; negative, absence of binding; nt, not tested.

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Comparison of PADI4 ChIP-chip with Elk-1 ChIP-chip dataset [33].

Xuesen Zhang (148860), Matthew J. Gamble (218822), Sonja Stadler (218828) et al. · Figshare · 2015

Comparison of PADI4 ChIP-chip with Elk-1 ChIP-chip dataset <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002112#pgen.1002112-Boros1" target="_blank">[33]</a>.

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