Haynes:UPLassay

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Universal Probe Library Assay

Based on the Universal ProbeLibrary Assay Quick Guide from Roche

Workflow Overview

1. Planning: Design your primers
2. Planning: Design your reactions
3. Wet bench: Make Gene Target master mixes
4. Wet bench: Make Template (cDNA) master mixes separately
5. Wet bench: Add the appropriate combinations of of the master mixes to the 96-well plate

---> Run the reaction in the Light Cycler!

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1. Design your primers

• Each gene you analyze requires a set of three oligos: forward primer, reverse primer, and a UPL probe.
• Use Roche's Assay Design Center to design optimal primers, and to identify the right UPL probe for your gene(s) of interest.
• The forward and reverse primers need to be ordered from a DNA synthesis company (e.g., IDT DNA, Promega, etc.), and the UPL oligo comes from Roche.

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2. Set up a reaction list and plan the plate layout

• How many reactions should I plan to run? Each experimental cDNA sample is a Template. The gene being detected is often referred to as a Gene Target. You should also include a reference Gene Target such as GAPD (a housekeeping gene that is always active, not expected to change). Each unique template and target combination requires its own reaction. You will also need to set up a no template control to observe the amount of background noise from that reaction.
• Hypothetical example:
  • cDNA samples + a no template control = 3
  • Gene targets + GAPD reference = 5
  • Replicates per reaction = 3
  • Wells needed = 3 * 5 * 3 = 45

REACTION LIST   Template cDNA Gene Target Rxn 1: treated cells MPK14 Rxn 2: treated cells CBX8 Rxn 3: treated cells TNF Rxn 4: treated cells NPPA Rxn 5: treated cells GAPD (reference gene) Rxn 6: untreated cells MPK14 Rxn 7: untreated cells CBX8 Rxn 8: untreated cells TNF Rxn 9: untreated cells NPPA Rxn 10: untreated cells GAPD (reference gene) Rxn 11: no template MPK14 Rxn 12: no template CBX8 Rxn 13: no template TNF Rxn 14: no template NPPA Rxn 15: no template GAPD (reference gene)

PLATE LAYOUT Variation 1 Variation 2 Both Variations (1 and 2) are correct. Choose a format that helps you to easily keep track of the samples. If you have a large experiment, try to fit as many reactions on the plate as you can (to avoid wasting plates), but also keep the samples arranged in an orderly fashion so that the set-up won't confuse you.

• A single plate contains 96 wells. To insure accuracy, three technical replicates per reaction (Rxn) are required
• If you need more than 96 wells, you must split the experiment over multiple plates.
• It is absolutely critical that you keep a reaction list and plate layout in your notes. Your plate set-up will probably vary for each run.

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3. Reaction set-up: PCR master mixes for each Gene Target

• Label one 1.5 mL tube per gene target
• Make enough PCR master mix for your plate...
  • MPK14 is in Reactions 1, 6, and 11 = 3
  • Replicates per reaction = 3
  • Master mix amount = 3 * 3 + 1 (to allow for pipetting error) = 10
  • The same needs to be done for CBX8, TNF, NPPA, and GAPD in separate tubes.

Reagent	(Single well)	Gene Target (x10)	GAPD (x10)
2x LC480 Probes Master	(7.5 μL)	75.0	75.0
20 μM Forward primer	(0.3 μL)	3.0	3.0 GAPD primers*
20 μM Reverse primer	(0.3 μL)	3.0	---
10 μM UPL probe	(0.3 μL)	3.0	3.0 GAPD UPL probe*
PCR H2O	(0.1 μL)	1.0	4.0
Total vol.	(8.5 μL)	85.0	85.0

*GAPD primer mix and the GAPD UPL probe are supplied in the Roche Universal ProbeLibrary Human GAPD Assay kit, #05190541001

Resulting 1.5 mL tubes:

• MPK14 - 85.0 μL
• CBX8 - 85.0 μL
• TNF - 85.0 μL
• NPPA - 85.0 μL
• GAPD - 85.0 μL

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4. Reaction set-up: master mixes for each Template

• Typically, you will have only 20 μL of stock cDNA on hand.
• Make a 1:10 dilution of cDNA by adding 10 μL of the stock cDNA to 90 μL of PCR H₂O.
• Make enough Template master mix for your plate...
  • Treated cells cDNA is in Reactions 1, 2, 3, 4 and 5 = 5
  • Replicates per reaction = 3
  • Master mix amount = 5 * 3 + 1 (to allow for pipetting error) = 16
  • The same needs to be done for templates "untreated cells" and "no template" in separate tubes.

Reagent	(Single well)	cDNA Template (x16)
1:10 cDNA dilution	(2.0 μL)	32.0*
PCR H2O	(4.5 μL)	72.0
Total vol.	(6.5 μL)	104.0

*For the no template control, use PCR H₂O instead of cDNA.

Resulting 1.5 mL tubes:

• T1 - treated cells cDNA, 84.5 μL
• T2 - untreated cells cDNA, 84.5 μL
• T3 - no template control, 84.5 μL

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5. Reaction set-up: loading the 96-well plate
The following illustrations use Plate Layout Variation 2...

Pipette 19.5 μL of cDNA Template master mixes into the first well of each 3-well group
Add 25.5 μL of Gene Target master mix to the cDNA. After each addition, mix by gently pipetting up and down 3 - 5 times (without making bubbles).
Transfer 15 μL of solution from A1 into A2, and A3. Use a fresh pipette tip to do the same for A4-6, and A7-8.
Repeat this procedure for the rest of the plate

• Seal the plate with clear film.
• The plate is now ready to load into the Light Cycler 480!