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
Sample details: rostral or caudal thirds of E11.5 C57 neocortex where pooled from three embryos. RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. "Single Step Method of RNA Isolation by Acid Guanidinium Thiocyanate-Phenol-Chloroform Extraction." Amplification and probe labelling were carried out as detailed in this paper: 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
Data processing
log ratios were lowess normalised, and filted to exclude (1) spots flagged as bad and (2) spots where 55% of the foreground pixels in either channel where less intense than the (background intensity + 1SD)
