Time course of DC3000 vs delta hrp on tomato Prf-3

Hybridization: DC3000/delta hrp 24h

Hybridization protocol
Hybridization solutionSDS Genisphere Hybridization Solution
Solution concentration0.25m NaPO4, 4.5%SDS, 1mm EDTA, 1x SSC, 2x Denhardt's Solution
Blocking agentssDNA and Oligo dT
Wash procedure2x15 minutes
1) 2x SSC + 0.2% SDS at 55 C.
2) 2x SSC at RT.
3) 0.2x SSC at RT (+ 0.5mM DTT)
Labeled Target Quantity6 ul labeled cDNA
Hybridization Time(1) 14 hours (2) 2 hours
Hybridization Volume65 ul
Hybridization Temperature60 C / 55 C for secondary hyb
Hybridization InstrumentCorning hybridization chambers in water bath

Scan information
Scan hardwareScan Array 5000
scan softwareScan Array ver 3.1

Image analysis information
SoftwareImaGene ver 5.1
Analysis algorithm1) Images
Cy5 = Red Cy3 = Green
Default settings for image analysis algorithms were used, according to manufacturer's protocol

Normalization information
Normalization softwaremarray package under R
Normalization algorithmPrint-tip specific Lowess Normalization
Normalization strategyTotal Array