Transcriptome analysis of the tomato-Clavibacter michiganensis subsp. michiganensis compatible interaction

Hybridization: Cmm 4d

Hybridization protocol
Hybridization solution1X hybridization buffer
Solution concentration100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween 20
Blocking agentHerring sperm DNA (final concentration 100ng)
Wash procedureAutomated fluidics station consisting of wash buffers A and B. Wash buffer A is a non-stringent buffer containing 6X SSPE, 0.01% Tween 20. Wash buffer B is a stringent buffer containing 100 mM MES, 0.1 M NaCl, 0.01% Tween 20
Labeled Target Quantity5 ug
Hybridization Time16 hours
Hybridization Volume80 ul
Hybridization Temperature45C
Hybridization InstrumentHybridization oven 640 (Affymetrix)

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