HuSNP chip

A group led by Lee and Buetow (28) describes an efficient approach to EAI analysis that uses Affymetrix HuSNP chips to assay for both sample genotype and allele-specific expression level. Of 602 informative (heterozygous) genes expressed in kidney or liver, 54% were found to show EAI in at least one of seven individuals tested. 

The HuSNP chip was washed and stained with the following Fluidics Protocol. 

We extracted the intensity values for each probe from the. CEL files generated by Affymetrix MAS 4.0. The. CEL files contain the fluorescent intensity values for each of the probes. HuSNP chip contains minimally 16 probes for each SNP locus. Pour of the 16 probes match perfectly to allele A, four to allele B, four have one mismatch to allele A, and the other four have one mismatch to allele B. Allele A and allele B represent the two alleles of the SNP. Each probe... 

Fig. 2. Scan image of a HuSNP chip. The scan image is from one of the genomic DNA HuSNP experiment. HuSNP 2k label should be clear.

We used Affymetrix MAS 4.0 in this study. A typical scan image is shown in Fig. 2. You should see a sharp image with HuSNP 2K label and signals evenly distributed across the chip. A report for the image is presented in Table 1. A1 to A21 correspond to 1 to 21 of the 24 multiplex PCRs (Fig. 1, lanes 1-21), which... 

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