Variations of ChIP

Different variations of ChIP experiments are now rapidly evolving. This is mainly due to the rapid progress in the field of microarrays and next-generation sequencing that can be used for the analysis of the immunopreciptated DNA. We discuss here the most important variations of the standard ChIP protocol with a focus on ChIP-on-chip and ChIP-sequencing technologies. 

The combination of chromatin immunoprecipitation with DNA microarrays allows the genome-wide analysis of the distribution of an antigen. The immunoprecipitated DNA is quantitatively amplified, labeled and used to probe DNA microarrays. In principle ChIP-on-chip methods can be divided into two basic groups, depending on the content of the microarrays which are used (i) microarrays/promoter tiling arrays and (ii) genome tiling arrays. 

In microarrays the probes are designed with a focus on specific genomic elements such as promoters. These promoter tiling arrays have the advantage that costs are reduced, but they are biased since array design relies on known aimotation. Thus, relevant regions may not be covered [20]. 

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Here we provide insight into the ChIP technique, the most important steps and some trouble-shooting guidelines. We describe the variations of ChIP and recent new developments, especially for genome-wide studies. We also focus on the data analysis, since in silico data analysis becomes more and more central for successful Chip experiments. In the last section we discuss two examples for data analysis based on recent publications. For detailed ChIP protocols we refer the reader to the excellent protocols database freely available at http //www.epigenome-noe.net/ researchtools/protocols.php. 

Chip-forms, Chip Breakabiiity and Chip Control, Fig. 6 Variation of chip-forming mechanisms in machining with the same tool insert (Sandvik 1996)... 

Chip-forms, Chip Breakability and Chip Control, Fig. 10 Variation of chip-form by up-curling and side-curling (Nakayama 1984)... 

The main bottleneck in the further development of CEC is related with the state of the art of the column manufacturing processes and the robustness of the columns/instrumentation. Moreover, evidence to demonstrate reproducibility of separations from column to column still has to be established. The formation of bubbles in the capillaries due to the Joule heating and variations in EOF velocity on passing from the stationary phase through the frit and into the open tube is still very challenging in packed column CEC. A way to overcome this problem is to use monolithic columns or apply open tubular CEC [108]. Currently, many efforts are placed in improving column technology and in the development of chip-CEC [115] as an attractive option for lab-on-a-chip separations. 

The performance of the temperature controller was measured in the tracking mode. Figure 6.18 shows a graph, where the temperature of one of the three microhotplates is kept at a constant temperature of 300 °C, the temperature of the second microhotplate is modulated using a sine wave of 10 mHz, while rectangular temperature steps of 150 °C, 200 °C, 250 °C, 300 °C, and 350 °C have been appHed to the third microhotplate. Temperature measurements on one of the hotplate that has been operated at constant temperature in the stabihzation mode showed a variation of less than 1 °C, even though the temperature of the neighboring hotplates was, at the same time, modulated dynamically (sine wave, ramp, steps). This is a consequence of the individual hotplate temperature control, without which thermal crosstalk between the hotplates would have been clearly detectable. The power dissipation of the chip is approximately 190 mW, when all three hotplates are simultaneously heated to 350 °C. In the power-down mode, the power consumption is reduced to 8.5 mW. 

Variations of semiconductor PL and EL intensities resulting from analyte adsorption are promising techniques for chemical sensing. When coupled with films such as MIPS, the selectivity of such structures may be improved. Integrated devices in which forward- and reverse-biased diodes are juxtaposed using microelectronics fabrication methods provide an opportunity to create completely integrated sensor structures on a single chip and to prepare arrays of such structures. 

Clever variations of electrophoresis allow us to separate neutral molecules as well as ions, to separate optical isomers, and to lower detection limits by up to 106. Adaptations of electrophoresis provide a foundation for new technology called analysis on a chip. In the future, drug discovery and clinical diagnosis will depend on small chips carrying out unprecedented numbers of operations with unprecedented speed. 

Fortunately, over the past several years, the problems associated with each of the above requirements have been overcome and now integrated opto-chips are now relatively routinely fabricated [2, 3, 5, 63, 64, 271-278, 290-297]. The problem of irregular VLSI surface topology has been overcome by use of planarizing polymers such as Futerrex PC3-6000. The reflow properties of this polymer reduce the 1-6 micron semiconductor circuit features to surface variations of 0.2 microns after planarization. The optical quality of planarized surfac-... 

If ICP-MS is used to measure Pb levels,care must be taken to sum the masses of 206, 207, and 208 m/z to account for the natural isotopic variation of Pb in the environment. Failure to sum masses can skew results above or below the actual concentration, as the isotopic abundance of a particular mass in the calibrator might not match the sample. However, this isotopic variation can be exploited to determine the source of Pb exposure. By determining the relative abundances of Pb in blood and also of potential sources of exposure (e.g., paint chips and soil), a matching pattern can be identified. The exposure source with the same ratio of major Pb isotopes as the blood should then be avoided or removed from the patient s environment. 

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