Hybridization of Panorama Gene Arrays
October 09, 2000
1. Rinse the blots in 50 ml of 2x SSPE for 5 minutes. Drain and
discard the solution.
2. Pre-warm the hybridization oven to 65oC. Warm the
hybridization solution to 65oC for about 10 min prior
to use. Pre-hybridize the Panorama gene array in 5.0 ml Hybridization
Solution for at least 1 hr at 65oC, using roller bottles
at 6 r.p.m. Note: Chemicals may come out of the hybridization
solution at storage of 4oC. Pre-warming to 65oC
ensures that all components are dissolved. Add Salmon sperm DNA
(final concentration of 100mg/ml) to pre-hyb and hybridization solutions
immediately prior to use.
3. Denature the 400-600 ml
cDNA generated probe (90-95oC for 10 min) and add to
3 mls hybridization solution.
4. Decant and discard the pre-hybridization solution from the array.
Add the denatured, labeled cDNA in the hybridization solution to
the array roller bottle (30cm x 3.5cm)
5. Hybridize overnight (12-18 hrs) at 65oC.
6. After hybridization, pre-warm the Wash Solution to 65oC.
7. Decant hybridization solution into P33 liquid waste.
8. Add 50 mls Wash Solution to the roller bottle. Wash the array
by inverting roller bottle at room temperature on the inverting
shaker for 5 minutes. Alternatively, hand roll the bottles for 5
minutes behind a radiation shield. Decant and discard the wash solution.
9. Repeat step 8 two more times
10. Add 80 ml Wash Solution & incubate/wash in hybridization
oven at 65oC for 30 min at 6 r.p.m.
11. Repeat step 10 two more times.
12. Decant Wash Solution and use forceps to gently pull out the
array (allowing the solution to run down the inside of the hybridization
tube).
13. Store the membrane. There are possible methods for doing this.
In both methods it is vital to keep the membrane moist.
Method 1
- Roll up the moist membrane and place it into a clear sheet protector.
- By rolling up the membrane it is much more manageable to place it
into the clear sheet protector.
- Once it is inside the sheet protector it can be easily unrolled.
- Take a glass pipet and roll it over the membrane inside the sheet
protector to push out bubbles thus ensuring the membrane is snuggly
surface tension retained to the sheet protector.
- Quickly seal around the membrane using a lab bag sealer (low setting
or you will melt through the plastic) to prevent any air bubbles
from entering.
Method 2
5x SSPE |
25ml of 20X SSPE Stock |
2% SDS |
20ml of 10% SDS Stock |
1x Denhardt’s Reagent |
2.0ml of 50X Denhardt’s Stock |
100 mg/ml sonicated,
denatured salmon sperm DNA |
100ml of 10mg/ml stock |
bring to 100ml with dH2O |
52.9ml dH2O |
Wash Solution (Makes 1 L)
0.5x SSPE |
25ml of 20X SSPE Stock |
0.2% SDS |
20ml of 10% SDS Stock |
bring to 1L with dH2O |
955ml dH2O |
20 X SSPE (3.6 M NaCl, 0.2M sodium phosphate, 20 mM EDTA)
(Makes 1 L. Store at 4oC)
210.42g NaCl
23.99g NaH2PO4
7.4g EDTA
in 800 ml nanopure H2O
Adjust to pH 7.7 with NaOH pellets. Adjust to 1 L with nanopure
water. Autoclave & store at 4oC.
50X Denhardt’s Reagent (1% Ficoll, 1% PVP, 1%BSA):
5g Ficoll ( MW 400,000)
5g polyvinylpyrrolidone (PVP; MW 40,000)
5g bovine serum albumin (BSA)
in nanopure dH2O to 500ml, filter sterilize and
store (-20oC)
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