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GenomiPhi amplification of FFPE tissue DNA for array CGH

8600 Variable Mode Imager inquire

Proteinase K, 100 mg E76230Y

SpectralChip™ 2600 BAC Array, 5 pack SC2600-5PK*

Constitutional Chip™ 1.0 BAC Array, 5 pack CC1.0-5PK*

*GE Healthcare is the exclusive distributor of Spectral Genomics products outside the United States and Canada.


Other materials required
FFPE human liver tissue (Asterand)

Chelex-100 resin (Bio-Rad)

DOP-PCR primers (Integrated DNA Technologies)

GenePix™ 4000B Microarray Scanner (Axon Instruments)

GenePix Pro 3.1 Microarray Image Analysis Software (Axon Instruments)

Thermal cycler (MJ Research)

Quant-iT™ PicoGreen™ dsDNA Assay Kit (Invitrogen)

HyperLadder I DNA ladder (BioLine)

Dpn
II restriction endonuclease (New England BioLabs)


Methods
DNA extraction from FFPE tissue slides
Genomic DNA was isolated using Chelex-100 from a 20-µm section of FFPE liver tissue. The detailed protocol is given below. DNA was quantitated using PicoGreen dsDNA quantitation reagent.

1. Add 2 µl of 10 mg/ml Proteinase K to each tube (final concentration 200 µg/ml).

2. Incubate at 55 °C for 3 h. Agitate gently every hour.

3. Add 100 µl of 5% Chelex-100 in Tris-EDTA.

4. Heat to 99 °C for 10 min.

5. Shake gently and spin at 10,500 x g for 15 min (while still hot).

6. Place on ice and remove any hard
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