3dgenome
  • Initial page
  • Cover
  • Preface
  • Figurelist
  • Chap0 Preparation
    • 0.1 Molecular biology
    • 0.2 Sequencing technologies
    • 0.3 RNA-seq Data Mapping & Gene Quantification
    • 0.4 RNA-seq Differential Analysis
  • Chap1 Why we care about 3D genome
    • 1.1 From 2D to 3D nuclear structure
    • 1.2 From static to dynamic
    • 1.3 From intra to inter chromosomes "talk"
    • 1.4 From aggregation to division - phase separation
  • Chap2 experiment tools for exploring genome interaction
    • 2.1 Image based
    • 2.2 Primary order
    • 2.3 Higher order C-techs
  • Chap3 Computational analysis
    • 3.1 Primary order analysis
    • 3.2 Higer order data analysis
      • 3.2.1 Read mapping consideration
      • 3.2.2 Analytical Pipelines
        • GITAR Pipeline
        • HiC-Pro Pipeline
      • 3.2.3 TAD calling algorithms
    • 3.3 3D structure
  • Chap4 RNA-genome interaction
    • 4.1 Experimental Methods
    • 4.2 Computational Analysis
  • Chap5 Integrative Data Visualization Tools
    • 5.1 GIVE
    • 5.2 HiGlass
  • Chap6 4DN Project
  • Appendix
    • Homework
    • Student's presentation
      • A Brief Introduction to Machine Learning
      • Precision medicine
      • CHIP-Seq
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On this page
  • Review of Molecular Biology
  • Question 1 (15 points)
  • DNA-seq
  • Questions 2 (15 points)
  • Question 3 (10 points)
  • RNA-seq
  • Question 4 (10 points)
  • Question 5 (20 points)
  • Question 6 (30 points)
  1. Appendix

Homework

Review of Molecular Biology

Question 1 (15 points)

a. Describe how polymerase chain reaction (PCR) work. (5 pts)

b. Describe how microarrays work. (5 pts)

c. Why is the central dogma incorrect/incomplete nowadays? (5pt)

DNA-seq

Questions 2 (15 points)

a. Describe how Sanger sequencing work. (10 pts)

b. What does the role of ddNTP play in Sanger sequencing? (5 pts)

Question 3 (10 points)

a. Describe how Illumina’s sequencing work. (10 pts)

RNA-seq

Question 4 (10 points)

a. Draw the typical structure of coding genes (5 pts)

b. Apart from coding genes, what are other annotated elements in genome? (5 pts)

Question 5 (20 points)

a. Describe five ways in which gene expression can be altered from Transcription to post-translation step. (5pt)

b. What is alternative splicing? (5pts)

c. If a gene has “x” number of exons, how many proteins could potentially be created? (5pts)

d. If exactly “y” exons are to be retained in the final transcript, how many proteins can be created? (5pts)

Question 6 (30 points)

a. Describe how experimental pipeline of RNA-seq works. (10 pts)

b. What are the steps of RNA-seq data analysis after RNA-seq run is performed (5 pts)?

c. What goals can RNA-seq analysis achieve (5 pts) ?

d. What are four pros and four cons of RNA-seq compared to microarray? (10 pts)

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Last updated 6 years ago