Effects of Potato Spindle Tuber Viroid on Tomato Gene Expression

Hybridization: PSTVd-MT (+BR)

Hybridization protocol
Hybridization solutionGeneChip Hybridization Cocktail
Solution concentration50pM Control Oligonucleotide B2, 10% DMSO, 1X Hybridization Mix, Hybridization Controls (1.5pM bioB, 5 pM bioC, 25 pM bioD, 100pM cre), .5mg/mL BSA, .1mg/mL Herring Sperm DNA
Blocking agentN/A
Wash procedurePost hybridization wash #1: 10 cylces of 2 mixes with Wash Buffer A @ 25C; Post hybridization wash #2: 8 cycles of 15mixes with Wash Buffer B @ 50C, Stain: Stain 10min SAPE @ 25C, Post Stain Wash: 10 cycles of 4 mixes with Wash Buffer A @ 30C, 2nd Stain: Stain probe array for 10min in Antibody Solution @ 25C, 3rd Stain: Stain probe array for 10min SAPE solution @ 25C, Final Wash: 15 cycles of 4 mixes with Wash buffer A @ 35C. Holding temperature is 25C.
Labeled Target Quantity5ug aRNA (Final Dilution .05ug/ul)
Hybridization Time16hrs
Hybridization Volume80ul
Hybridization Temperature45C
Hybridization InstrumentHybridization Oven 640

Scan information
Scan hardwareAffymetrix GeneChip Scanner 3000 7G
scan softwareAffymetrix GeneChip Command Console software

Image analysis information
SoftwareAffymetrix GeneChip Operating Software (GCOS)
Analysis algorithmMAS 5 software

Normalization information
Normalization softwareMAS 5
Normalization algorithmN/A
Normalization strategyScaling