Date 9/12/2000 Original sample Species : Mouse Strain : CD-1 (outbred) Genotype : wild-type Stage : 8 d.p.c., Theiler stage 12 Tissue : embryo proper Treatments applied Agent : 2-chloro-2'-deoxyadenosine Route : single i.p. injection Dose : 2.5 mg/kg Time : 3 hrs post-injection Intervention : none Risk: benchmark dose modeled for 5% increased risk of microphthalmia Conditional biomarker: weak p53 protein induction observed or anticipated Technical extraction & labeling Tissue procurement : conventional microdissection Sampling unit : 8-10 embryos pooled from same litter Hybridization extract preparation : 2-4 ug total cellular RNA (Qiagen RNeasy kit Cat. 74103) Labeling (cDNA) : dinitrophenol-11-dCTP, biotinyl-11-dCTP Hybridization condition : 56oC, overnight, stringency washes 0.5X SSC, 0.1% SDS, 0.06X SSC, 0.01% SDS, and 0.06X SSC Detection & raw data organization Immunodetection : anti-DNP with Cy3-tyramide, peroxidase-conjugated streptavidin with Cy5-tyramide Scanning : Micromax Custom Scanning and Data Processing Service (PerkinElmer Life Sciences, Cat.MPS401), Cy3 channel 532 nm and Cy5 channel 635 nm Spot measurement : ImaGene Method 1: Calculates average intensity of all pixels within the circle with intensity values falling in the predetermined range (e.g., 50% - 95% of maximal intensity in a grid square of a spot). Background correction : The background is calculated from the background range of pixels (e.g., 5-15% of maximal intensities) between the background rings. Local background is the subtracted from signal from every spot and every channel separately. Gene expression matrix : 2400 element array less 12 control spots and 6 spots from incomplete printing resulting in 2382 spots
