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In order to search gene candidates involved in TTX accumulation in the torafugu pufferfish Takifugu rubripes, a custom 4x44k oligonucleotide microarray slide was designed by the Agilent eArray program using oligonucleotide probes of 60 bp in length referring to 42,724 predicted transcripts in the publicly available Fugu genome database.
Each microarray slide was hybridised with a 1∶1 mixture of sample and control cDNAs, each labelled with a different dye.
Following incubation, the microarray slide was washed for 5 minutes in aCGH/ChIP-on-chip Wash Buffer 1 (0.5X SSPE, 0.005% N-lauroylsarcosine; room temperature) and 5 minutes in a CGH/ChIP-on-chip Wash Buffer 2 (0.1X SSPE, 0.005% N-lauroylsarcosine; 31°C).
The microarray slide was placed probe side towards the target.
Thereafter, the microarray slide was scanned using Agilent Microarray Scanner G2505B.
Data from each microarray slide was normalized using print-tip loess.
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After stringent washing, microarray slide is then subjected to fluorescence scanning.
Replicate spots per microarray slide were summarised by calculating the arithmetic mean (Microsoft Excel 2003).
The rSEPs on the microarray slide were probed using patient sera according to previous descriptions [ 9].
Pre-hybridization of microarray slides was previously described [24].
data of four microarray slides was used.
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