The SNP Array 6.0 platform has three check points prior to hybridization on GeneChip arrays in order to remove samples with experimental errors.
The CMap annotation file (cmap_instances_02.txt) indicates the distinct instance ID for each pair of treatment-control samples with experimental conditions (i.e., concentration, cell line, and batch).
The resulting octal codes from both in silico approaches were identical for 42 (95.5%) of the 44 samples with experimental results (see Supplementary Table S1 for detailed results).
We thank Sylvie Benestad (National Veterinary Institute, Oslo, Norway) for Nor-98 sheep samples, and Danny Matthews (VLA, Weybridge, UK) for the sheep sample inoculated with experimental cBSE.
Twenty-nine sasples, as well as 4 of the 10 samples compatible with experimental BSE and 9 samples with low levels of PrPres, were previously identified as atypical scrapie (open bars, Figure 3).
Having established that we could observe PIX in a sample with our experimental protocol using the "positive control", we examined purified P-gp reconstituted in liposomes.
Hemocytometer counts of semen samples diluted with experimental FSW were used to determine the amount of sperm solution required to achieve a final sperm to egg ratio of 500 1; 1 × 10 sperm/mL.
Minus RT samples tested simultaneously with experimental samples by quantitative RT-PCR with Sybr Green consistently yielded no amplification below 30 cycles using the above protocol.
Tubes containing supplemented medium but no tissue were incubated, sampled, and analyzed along with experimental samples to serve as assay blanks.
