Welcome to Tuesday!

  1. Take a minute to look at today’s questions and rate your knowledge

  2. Then, in your group discuss:


Monday’s questions

  1. How many million CpG sites are there in the human genome?
  1. 28k
  2. 1M
  3. 28M
  4. 150M
  1. Which method does not provide DNA methylation estimates at a base-pair resolution?
  1. EPIC array
  2. RRBS
  3. MeDIP-seq
  4. WGBS
  1. What is the main purpose of treating DNA with bisulfite conversion?
  1. To denature DNA
  2. To convert unmethylated cytosine (5C) to uracil
  3. To convert metylation cytosoines (5mC) to thymine
  4. To prepare DNA for NGS library preparation
  1. What is the major difference between long-read (PacBio/ONT) and short-read (Illumina) NGS for measuring DNA modifications
  1. Short read NGS can directly detect 5mC in DNA
  2. Long-read NGS required bisulfite treatment prior to sequencing
  3. There is no difference between short-read and long-read sequencing platforms when it comes to measuring base modifications
  4. Long read NGS can directly detect several different base modifications in DNA
  1. Which metric would you use to visualize methylation data from the 450K array?
  1. The Beta-value
  2. The M-value
  3. Both can be used
  4. The signal intensities
  1. Why perform within-array normalization?
  1. To remove the background noise
  2. To remove failed beads
  3. To remove differences between probe design I and II
  4. To make samples more comparable across samples
  1. What complicates gene enrichment analysis for methylation data?
  1. The link between CpG and gene is not always clear
  2. The effect of methylation on gene expression is hard to predict
  3. There is a bias related to the number of CpG per gene
  4. All of the above
  1. Which genome structure is preferentially studied through reduced representation bisulfite sequencing?
  1. Gene bodies
  2. CpG Islands
  3. CpG Shores
  4. Enhancers