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Vesa Turkki designed, conducted, and analyzed in vitro experiments, in vivo experiment, ChIP, and ChIP-sequencing studies.
We have presented the novel use of SNP-arrays for identification of DNA fragments in a chromatin immunoprecipitation experiment (ChIP on SNP-chip).
A user can choose the experiment, chip, gene and analysis software to be used in a step-by-step process, following which the related samples can be labelled and organized for an easy comparison through histograms or radar-graph representations.
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The application of high-throughput (HTP) DNA sequencing to ChIP experiments (ChIP-seq) has overcome many microarray-related limitations in probe coverage and resolution [10] [13].
In a parallel experiment, ChIP-seq was also carried out for H3K27me3 using non cross-linked chromatin from wildtype C24 seedlings.
Our analysis of in vivo c-Myc sites detected in a chromatin immunoprecipitation with the paired-end ditag experiment (ChIP-PET) (Zeller et al. 2006) revealed that CpG deamination driven creation events make up as much as 56% of noncanonical and 28% of canonical c-Myc site creation events, and as expected, they are localized at positions 2, 3, 4, and 5 within c-Myc motifs (fig. 2 A and table 1).
In the experiments chip geometry, forces and tool wear are measured.
In addition to drug experiments, chip platforms are applicable to neuropathology research.
In these experiments, chips covered with human DNA corresponding to various genes were coated with both human and chimp RNA.
The chromatin immunoprecipitation experiments (chip-CHIP experiments) from which the TF-gene interactions were acquired were garnered from [ 49, 50].
In both experiments ChIP-seq library was obtained using Illumina Solexa ChIP-seq sample processing methods.
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