7.342: Week 8 Questions

Post discussion, questions, or comments about the Week 8 course material here.

Amber
Davis et al: Figure 5's Northern blot has bands that are huge. Did they leave it exposed too long to magnify the bands that show up less?

Blais et al: What is happening in Figure 4A?

Georgi
Blais et al. Has an analogous whole genome-wide study been done? They have only ~4700 promoters on their array which is not that many

Holly
Blais et al. What are position weight matrices and what is the CREME algorithm?

Davis et al. What is the role of myoA and myoH? How does growth arrest in 10T1/2 cells induce their expression? Presumably the signalling following growth arrest differs in different cell lines (as myoA and myoH aren't expressed in all growth arrested cells). Since myo D is not expressed in any of these cells it probably isn't the cause of the difference. What is?

Kathy
Davis: I'm having trouble following their subtracted cDNA hybridization. Is the idea is to get myoblast-specific cDNA by subtracting out the 5-azacytidine-treatment-specific cDNAs? How are they doing this subtraction?

Blais: Could we go over ChIP-chip again? How does this make a better prediction than regular microarrays/expression profiling? Wouldn't it miss some targets that do not involve chromatin modifications?

Manpreet
Blais et al: The authors talk about sorting by gene function, using Gene Ontology notation. What is this, and could you explain how its done?

Davis et al: I'm not sure I understand how 5-azacytidine works. Is it correct that its encorporated into DNA, and causes DNA demethylation? If so - how exactly is it encorporated into DNA?

Zak
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