See Livesey, F. J., Furukawa, T., Steffen, M. A., Church, G. M. and Cepko, C. L. (2000). Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx. Curr Biol 10, 301-10
Scan protocol
Hybridised microarrays were scanned on a GenePix 4000B microarray scanner and the resulting images were analysed with GenePix 5 array analysis software
Description
RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ug of total RNA was amplified by global poyadenilated PCR method in two parallel reaction. DNA replica1 was labeled with Cy3, DNA replica2 was labeled with Cy5 followed by co-hybridization on microarray slide.
Data processing
Limma packadge: log-ratio were lowess normalized, filtered to exclude spots flagged as bad and backgroud corrected.
