Chips, ChIP-chips, ChIP-seqs, other seqs, and, um, reporter genes

Biotechnology Chapter 8 Day 2 Questions

1. Briefly discuss whole-genome tiling arrays, quasi-whole-genome arrays, splice junction arrays, and exon scanning arrays.
2. For humans, only a chromosome 21 and chromosome 22 whole genome array is available. Why these chromosomes?  What did the book mention was learned from this platform?  What technology has supplanted whole genome arrays?
3. Compare ChIP-chip and ChIP-seq.
4. What is the outcome of having a gene that is heavily methylated? View the bisulfate-treated DNA results in figure 1 of the Nobel-prize winning work for the creating induced pluripotent stem cells (iPSCs).  What would you conclude about the variety of genes that are active in embryonic stem cells, iPSCs, and fibroblasts?
5. Briefly discuss each of the major advantages of RNA-seq (a-h). What were the disadvantages of RNA-seq compared to whole-genome tiling arrays?  Can these disadvantages be mitigated?
6. Most of the time, scientists use “Poly(T) beads” in their workflow for RNA-seq. Why?  What could be missed by including this step?
7. How does a reporter gene work? How can this concept be modified to report the activity of a specific transcription factor?