5: Cloning and Sequencing
Gene cloning, DNA sequencing methods, and RT-qPCR.
Gene Expression Fold Change from RT-qPCR Data
Click to show Gene Expression Fold Change from RT-qPCR Data example problem
| Untreated Cells | Cells Treated with Experimental Drug | |||
| House Keeping Gene | Gene of Interest | House Keeping Gene | Gene of Interest | |
| Well 1 | 20.7 | 25.7 | 21.3 | 24.1 |
| Well 2 | 20.3 | 25.1 | 20.5 | 24.7 |
| Well 3 | 20.8 | 25.2 | 21.7 | 24.9 |
| mean Ct | 20.6 | 25.3 | 21.2 | 24.6 |
| ΔCt | ||||
| ΔΔCt | ||||
Given the data in the table above calculate the fold change (2|ΔΔCt|) value for the effect of the drug on the cells.
Note: answers need to be within 3% of the correct number to be correct.
True/False Statements About Long-Distance PCR
Click to show True/False Statements About Long-Distance PCR example problem
Which one of the following statements is FALSE of Long Distance PCR?
True/False Statements About PCR Components
Click to show True/False Statements About PCR Components example problem
Which one of the following is NOT a component in a typical modern polymerase chain reaction (PCR) experiment?
True/False Statements About Efficient PCR Primers
Click to show True/False Statements About Efficient PCR Primers example problem
Which one of the following statements is TRUE regarding PCR primers that are efficient and avoid mispriming?
True/False Statements About PCR Step Order
Click to show True/False Statements About PCR Step Order example problem
Which one of the following is the CORRECT order of steps in a polymerase chain reaction (PCR) reaction?
Degenerate Primer Codes from Sequence Alignments
Click to show Degenerate Primer Codes from Sequence Alignments example problem
| G | A | T | , | C | C | T | , | C | T | T |
| C | C | G | , | C | C | T | , | A | T | T |
| G | G | G | , | A | T | T | , | A | T | T |
| C | C | C | , | C | T | T | , | C | T | T |
| C | G | G | , | A | A | T | , | G | G | G |
| C | A | C | , | G | T | T | , | G | G | T |
| C | A | G | , | G | C | T | , | C | G | T |
| G | A | T | , | C | C | T | , | A | G | G |
| G | C | T | , | G | A | T | , | A | T | G |
| G | A | T | , | G | A | T | , | A | G | T |
What is the arbritrary sequence code for degenerate primer design in the table above?
You may include a comma every 3 letters, but do NOT include any extra commas or spaces in your answer.
Consensus Sequences from Simple Alignments (Fill in the Blank)
Click to show Consensus Sequences from Simple Alignments (Fill in the Blank) example problem
| C | C | G | , | T | A | T | , | C | G | C |
| C | A | G | , | C | A | C | , | T | G | C |
| C | A | A | , | A | G | G | , | C | G | C |
| G | A | G | , | G | A | G | , | C | G | A |
| C | T | G | , | G | C | G | , | G | T | G |
| A | G | T | , | G | A | G | , | C | A | T |
| T | A | G | , | G | A | G | , | C | G | C |
| C | A | C | , | G | A | A | , | A | G | C |
| C | A | G | , | G | T | G | , | C | C | C |
What is the consensus sequence for the table above?
you may include a comma every 3 letters, but do not include any extra commas or spaces in your answer.
Consensus Sequences from Tables (Fill in the Blank)
Click to show Consensus Sequences from Tables (Fill in the Blank) example problem
| C | G | A | , | A | C | A | , | T | T | A | , | A | A | C |
| G | G | A | , | T | G | G | , | T | G | T | , | C | A | C |
| C | G | T | , | T | G | T | , | T | G | C | , | C | A | A |
| C | C | G | , | C | C | G | , | G | G | C | , | A | A | A |
| A | G | A | , | T | T | G | , | T | G | C | , | G | G | C |
| G | C | G | , | A | T | C | , | G | G | T | , | A | A | G |
| A | T | G | , | A | G | C | , | T | A | C | , | A | C | C |
| C | G | G | , | G | A | G | , | T | G | G | , | G | C | A |
| T | G | C | , | T | G | G | , | A | C | C | , | A | T | C |
What is the consensus sequence for the table above?
you may include a comma every 3 letters, but do not include any extra commas or spaces in your answer.
Consensus Sequences from Alignments (Multiple Choice)
Click to show Consensus Sequences from Alignments (Multiple Choice) example problem
What would be the consensus sequence for the following aligned sequences?
| G | C | G | , | G | G | C | , | A | A | C |
| G | G | G | , | C | C | A | , | G | C | C |
| G | T | G | , | T | A | T | , | T | G | G |
| G | C | A | , | T | A | C | , | G | G | C |