Here are some additional “bad examples” for more practice. If you haven’t already, make sure you first look at all the completed examples in lessons 1, 2, and 3, with more examples on the worksheets.
Given the aspects of subunit heterogeneity, their dimerization and DNA binding rules, the control of transcription of AP-1 subunit genes, the time course of subunit synthesis as well as degradation, and the regulation of their function become important issues for an evaluation of the effect on target gene expression and on cellular behavior.
We performed ChIP-qPCR experiments and validated seven randomly selected ChIP-chip peaks that were missing in the sequencing data. Either a lack of probe coverage on the array or higher sensitivity of ChIP-seq relative to array contributed to those ChIP-seq-specific-peaks.
There are many factors that can lead to poor library quality, such as poor anibody quality, over-cross-linking, an insufficient amount of starting material of ChIP DNA, inappropriate sonication and overamplification by PCR.
DNA methylation (DNAm) plays diverse roles in human biology, but this dynamic epigenetic mark remains far from fully characterized.
Our comprehensive overview of the experimental shortcuts that have been found in the different model organism communiteds and the new field of high-throughput assays should help during the preparation phase of a screen for enhancers.
Hydroxyapatite chromatography was introduced in 1956, but despite numerous publications describing its merits as a unique chromatography tool, it has failed to attain the popularity of ion exchange (Tiselius et al. 1956).