Dinh:Protocols/Probes Prep Nov24: Difference between revisions
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To use KAPA qPCR kit on CpG30K probes set, using reaction volume of | To use KAPA qPCR kit on CpG30K probes set, using reaction volume of | ||
25ul | 25ul | ||
To practice QUBIT DNA quantification | To practice QUBIT DNA quantification | ||
To create a probes preparation/purification table | To create a probes preparation/purification table | ||
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==Step 1: PCR Amplification == | ==Step 1: PCR Amplification == | ||
Reaction Mix | Reaction Mix: | ||
{| border="1" | {| border="1" | ||
!Reagent | !Reagent | ||
Line 31: | Line 30: | ||
!Vol (1x) | !Vol (1x) | ||
!Vol (8x) | !Vol (8x) | ||
!Vol (100x) | |||
|- | |- | ||
|ddH20 | |ddH20 | ||
Line 36: | Line 36: | ||
|11.806ul | |11.806ul | ||
|94.5ul | |94.5ul | ||
|1180.6ul | |||
|- | |- | ||
| 2x KAPA qPCR Master Mix | | 2x KAPA qPCR Master Mix | ||
Line 41: | Line 42: | ||
|12ul | |12ul | ||
|96ul | |96ul | ||
|1200ul | |||
|- | |- | ||
|AP1V4IU (100uM) | |AP1V4IU (100uM) | ||
|0.3uM | |0.3uM | ||
|0.072ul | |0.072ul | ||
|0.58ul | |0.58ul | ||
|7.2ul | |||
|- | |- | ||
|AP2V4 (100uM) | |AP2V4 (100uM) | ||
Line 51: | Line 54: | ||
|0.072ul | |0.072ul | ||
|0.58ul | |0.58ul | ||
|7.2ul | |||
|- | |- | ||
|Template CpG30k (20uM) | |Template CpG30k (20uM) | ||
Line 56: | Line 60: | ||
|0.05ul | |0.05ul | ||
|0.4ul | |0.4ul | ||
|5ul | |||
|- | |- | ||
!Total | !Total | ||
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|24ul | |24ul | ||
|192ul | |192ul | ||
|2400ul | |||
|} | |} | ||
Revision as of 19:30, 25 November 2009
November 24, 2009
KAPA SYBR FAST qPCR Kit Master Mix (2x) Universal
ideally suited for gene expression analysis low copy gene detection microarray validation gene knockdown validation
Notes:
protect kit components from light always ensure that the product has been fully thawed and mixed before use do not exceed 25 ul reaction volumes do not exceed 20ng template DNA per 24 ul reaction volume novel enzyme in kit enhances the amplification efficiency of both high GC and AT templates Chromo4 RT Detector does not require ROX Reference dye
Objectives:
To use KAPA qPCR kit on CpG30K probes set, using reaction volume of 25ul To practice QUBIT DNA quantification To create a probes preparation/purification table
Previous methods to quantify probes concentration at each purification steps included Nanodrop and PAGE quantification. However, Nanodrop quantification is inaccurate after ethanol precipitation. The drawback to PAGE quantification is that it cannot determine the total DNA concentration. I will use QUBIT and PAGE to determine the efficiency of each probes preparation step.
Step 1: PCR Amplification
Reaction Mix:
Reagent | Final Conc. | Vol (1x) | Vol (8x) | Vol (100x) |
---|---|---|---|---|
ddH20 | 11.806ul | 94.5ul | 1180.6ul | |
2x KAPA qPCR Master Mix | 1x | 12ul | 96ul | 1200ul |
AP1V4IU (100uM) | 0.3uM | 0.072ul | 0.58ul | 7.2ul |
AP2V4 (100uM) | 0.3uM | 0.072ul | 0.58ul | 7.2ul |
Template CpG30k (20uM) | 0.33pg | 0.05ul | 0.4ul | 5ul |
Total | 24ul | 192ul | 2400ul |
2. Program
94C - 30 s 94C - 3 s 60C - 30 s Plate Read Cycle to 2 for 40 more times 72C - 5 min 15C - forever end
3. Stopped at X cycles.