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Reference Gene qPCR

Goals

  • Determine which of your reference genes you are going to normalize to.

Why am I doing this?

Reference genes need to be stable across your control and experimental samples in order to be useful. If expression between the two differs, you will be normalizing to two different values and that is worthless. This is a common omission. Reference genes must be validated.

Typical plate setup for three candidate reference genes:

1

2

3

4

5

6

7

8

9

A

C1BR1

C1BR1

C1BR1

C1BR1

C1BR1

C1BR1

C1BR1

C1BR1

C1BR1

B

C1BR2

C1BR2

C1BR2

C1BR2

C1BR2

C1BR2

C1BR2

C1BR2

C1BR2

C

C1BR3

C1BR3

C1BR3

C1BR3

C1BR3

C1BR3

C1BR3

C1BR3

C1BR3

D

C1BR4

C1BR4

C1BR4

C1BR4

C1BR4

C1BR4

C1BR4

C1BR4

C1BR4

E

C1BR5

C1BR5

C1BR5

C1BR5

C1BR5

C1BR5

C1BR5

C1BR5

C1BR5

F

C2BR1

C2BR1

C2BR1

C2BR1

C2BR1

C2BR1

C2BR1

C2BR1

C2BR1

G

C2BR2

C2BR2

C2BR2

C2BR2

C2BR2

C2BR2

C2BR2

C2BR2

C2BR2

H

C2BR3

C2BR3

C2BR3

C2BR3

C2BR3

C2BR3

C2BR3

C2BR3

C2BR3

I

C2BR4

C2BR4

C2BR4

C2BR4

C2BR4

C2BR4

C2BR4

C2BR4

C2BR4

J

C2BR5

C2BR5

C2BR5

C2BR5

C2BR5

C2BR5

C2BR5

C2BR5

C2BR5

ref gene 1

ref gene 2

ref gene 3

C1 = CONDITION 1

C2 = CONDITION 2

BR# = BIOLOGICAL REPLICATE #

Conditions

What you are looking for

  • Technical replicates with a standard deviation below 0.2 (this is arbitrary and most of your replicates will be below 0.1. If you do enough qPCR, you will eventually become obsessed with how low you can get this number).
  • At least 2 reference primer sets that show no significant difference between control and experimental conditions. The standard deviation of the Cqs for all biological replicates should be low. (Preferrably Less than 0.5)
  • If you are seeing differences between replicates or perhaps conditions, you may be asking the question “how do I know if there’s really a difference, it could be something else like loading or RT-PCR efficiency? I am not controlling for any of these by normalizing to anything!”. The answer is if you prepared good quality RNA and loaded exactly the same amount of RNA into a well-prepared reverse transcription, there should be very little (less than 1 Cq) difference between biological replicates of the same condition, assuming that condition itself is reproducible. If the biological variation is truly large between replicates, you’ll have to pick the best you can.

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Topic revision: r1 - 21 Mar 2019 - 21:51:06 - Main.KateElston
 
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