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reads for each sample were retained and used for further analysis.
Only alignments with a single copy from each sample were retained, and several of these exons were partial.
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Twenty percent of each sample was retained as a 'Total' fraction, and precipitated in 4 volumes of methanol.
A 5 µL aliquot of each sample was retained to measure total bisulfite treated DNA using the real-time PCR assay (HB14) described in Supplementary Table S1.
A 5 µL aliquot of each sample was retained to measure total genomic DNA using the real-time PCR assay (CFF1) described in Supplementary Table S1.
Approximately 40 μl of each sample was retained as 'total input'.
At this stage a 50 μl aliquot of each sample was retained and boiled in Laemmli electrophoresis buffer [ 14] as input controls.
Cells in the residual volume of the initial sample were retained and used for controls.
Only genes for which acceptable data were obtained in at least 70% of the samples and that showed at least a 1.5-fold difference in expression from the mean for at least 1 sample were retained.
The heterozygous SNP loci in matched normal sample were retained for this analysis.
An average of 5 × 10 events per sample were retained after this step.
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