QPCR

Materials

• cDNA: see First Strand cDNA Synthesis (AB Kit) for details
• SYBR Green PCR Master Mix Applied Biosystems (ThermoFisher Catalog # 4367659; Vendor Link)
• 384 well qPCR plate (ThermoFisher Catalog # 4309849) and covers (Catalog # 4360954)
• Primers (Dilute to 0.4 uM mixture of fwd and rev. From 100 uM stocks- the 100uM stock is prepared by adding 227 uL of distilled water to 22.7nmol of a gene as an example- this is 4uL Forward Primer, 4 uL Reverse Primer and 992 uL Water). This primer mix can be stored at -20 in a Working Primers box. Design primers according to Primer Design for qPCR

Plate Preparation

1. Book 2h on qPCR machine by signing up on the sheet in room 6041
2. Prepare cDNA and dilute in water in a 96 well plate. Typically a 20x dilution of cDNA leaves enough to be detected.
3. Get optically clear 384 well plate and keep on paper towel. Do not touch bottom of plate.
4. Sketch out the plate in your notes. Typically rows are different primers while columns are different cDNA's
5. Calculate how many samples x how many replicates/per sample (start with 3 or 4 until you are consistent enough technically to decrease). This will be the number of wells need for each primer.
6. Prepare a Primer/SYBR Green mixture for each primer. For each well you will need 5 uL SYBR green + 2.5 uL Primer working stock, so if you have calculated you need 10 wells per primer that is 50 uL SYBR Green + 25 uL Primers. Make up 10-20% more than you need.
7. Using the repeater multichannel pipettor put on 2 or 3 tips (depending on your plate arrangement) and set to suck up however many samples you have and dispense 7.5 uL per well.
8. Dispense 7.5 uL of Primer/SYBR mixture into each well, dispensing at the bottom of the well.
9. Using the ClipTip multichannel add 2.5 uL of cDNA to each applicable well. You don't need to change tips between wells.
10. Once the plate is completed, carefully put an optically clear cover on it using the plastic square to ensure the edges are sealed, being very careful not to leave fingerprints on the seal.
11. You can prepare the plate ~3h beforehand, keeping it at 4C until the machine is ready.
12. Immediately before the run spin the plate briefly (2 mins at 4000 RPM) in the swinging bucket centrifuge.

Run Protocol

• Set up run using Thermo Cloud/QuantStudio or Roche LightCycler

see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC55695 for considerations on calculations