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AccessionType
normalization data transformation protocol
Data for both channels were Lowess-normalized and then log(2) ratio was taken ID_REF = Spot Reference ID VALUE = log2_ratio of CH2DL_MEAN over CH1DL_MEAN (LOG_RAT2L_MEAN) SPOT = spot number on array CH1_MEAN = CH1_SD = standard deviation of channel 1 intensity CH1_BKD_MEDIAN = channel 1 background median intensity CH1_BKD_SD = standard deviation of channel 1 background median intensity CH2_MEAN = channel 2 mean intensity CH2_SD = standard deviation of channel 2 intensity CH2_BKD_MEDIAN = channel 2 background median intensity CH2_BKD_SD = standard deviation of channel 2 background median intensity TOT_BPIX = number of background pixels TOT_SPIX = number of spot pixels CH2BN_MEDIAN = channel 2 normalized background median intensity CH2IN_MEAN = channel 2 normalized mean intensity CH1DL_MEAN = channel 1 Lowess_normalized mean intensity CH2DL_MEAN = channel 2 Lowess_normalized mean intensity LOG_RAT2N_MEAN = log2_ratio of channel 2 normalized over channel 1 (global normalization) CORR = correlation coefficient among pixels FLAG = Spot flag. 0:not flagged; negative:flagged as bad spots; positive:flagged as good spots
array scanning protocol
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.
hybridization protocol
described in Hu et al., 2005, BioTechniques, 38:121-128
hybridization protocol
described in Hu et al., 2005, BioTechniques, 38:121-130
hybridization protocol
described in Hu et al., 2005, BioTechniques, 38:121-142
labelling protocol
described in Hu et al., 2005, BioTechniques, 38:121-142
nucleic acid extraction protocol
Qiagen Rneasy Kit
hybridization protocol
described in Hu et al., 2005, BioTechniques, 38:121-140
labelling protocol
described in Hu et al., 2005, BioTechniques, 38:121-140
hybridization protocol
described in Hu et al., 2005, BioTechniques, 38:121-141
labelling protocol
described in Hu et al., 2005, BioTechniques, 38:121-141
hybridization protocol
described in Hu et al., 2005, BioTechniques, 38:121-139
labelling protocol
described in Hu et al., 2005, BioTechniques, 38:121-139
hybridization protocol
described in Hu et al., 2005, BioTechniques, 38:121-138
labelling protocol
described in Hu et al., 2005, BioTechniques, 38:121-138
hybridization protocol
described in Hu et al., 2005, BioTechniques, 38:121-137
labelling protocol
described in Hu et al., 2005, BioTechniques, 38:121-137
hybridization protocol
described in Hu et al., 2005, BioTechniques, 38:121-136
labelling protocol
described in Hu et al., 2005, BioTechniques, 38:121-136
hybridization protocol
described in Hu et al., 2005, BioTechniques, 38:121-135
labelling protocol
described in Hu et al., 2005, BioTechniques, 38:121-135
hybridization protocol
described in Hu et al., 2005, BioTechniques, 38:121-134
labelling protocol
described in Hu et al., 2005, BioTechniques, 38:121-134
hybridization protocol
described in Hu et al., 2005, BioTechniques, 38:121-133
labelling protocol
described in Hu et al., 2005, BioTechniques, 38:121-133