cubated at 37 C, 160 r m for 1 h, then cultured on SOB MgCl2 soli

cubated at 37 C, 160 r m for 1 h, then cultured on SOB MgCl2 solid media with ampicillin to generate the primary cDNA libraries. The transformed white bacteria were randomly picked and grown on 384 well plates containing Luria Broth li quid media with ampicillin at 37 C overnight. Glycerol was added for storage at ?80 C. A total of 8,000 cDNA clones were randomly picked from forward and reverse SSH libraries and used as for subsequent PCR templates. Each PCR was performed in a 100 ul reaction mixture using nested primers of SSH according to. The PCR products were precipitated with equal amount of isopropyl alcohol and washed with 75% ethanol, then re suspended in 40 ul sterile water. The yield and quality of the PCR products were determined by Nanodrop 1000 spectrophotometer, and then run on 1.

2% agarose gel and examined by Bio Rad UV spec troscopy to confirm single clone. Fi nally the validated PCR products were stored at ?80 C for custom microarray. Microarray slides fabrication and preparation GSK-3 of fluorescent dye labelled cDNA About 40 microlitre of PCR products were re precipitated by adding 100 ul of anhydrous ethanol and were dissolved in EasyArrayTM spotting solution at a final concentration of 0. 1 0. 5 ug ul 1 and then printed on amino silaned glass slides with a SmartArrayerTM microarrayer. Each clone was printed triplicate. The particular procedures for microarray fabri cation were conducted according to. The relative gene expression profiles of QS at four de velopmental stages compared with the corresponding four stages of EG were investigated by microarray analysis.

For each stage, three sets of total RNA samples were extracted independently, and then RNA pool was constructed by mixing aliquot of RNA from the three sets of RNA samples. An aliquot of 5 ug total RNA from the RNA pool was used to produce Cy5 Cy3 labelled cDNA employing an RNA amplifica tion combined with Klenow enzyme labeling strategy according to the protocol by. Cy5 Cy3 labelled cDNA was hybridized with the microarray at 42 C over night. Hybridization was performed in duplicate by dye swap. And then the arrays were washed with 0. 2% SDS, 2 �� SSC at 42 C for 5 min, and 0. 2% SSC for 5 min at room temperature. Microarray data analysis and EST sequence analysis Arrays were scanned with a confocal laser scanner, LuxScanTM scanner and the resulting images were analyzed with LuxScanTM 3.

0 software. cDNA spots were screened and iden tified with the methods described by. A spatial and intensity dependent normalization method was employed and normalized ratio data were then log transformed. Differentially expressed genes were identified using a t test, and multiple test corrections were performed using FDR. Genes with FDR 0. 05 and a fold change 2 were identified as differentially expressed genes. All the clones differentially expressed in at least one of the four stages were subjected to single pass sequence using standard high throughput sequencing by BGI Wuhan, China. All

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