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Indels in the entire genome were quantified using this output.
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TGEV genome copy numbers were quantified using a TaqMan fluorescent quantitative (q) PCR assay as previously shown [ 25].
Following successful recovery, the barcodes were quantified using a Genome Analyzer IIx (Illumina) and the GexSeqN sequencing primer at a final concentration of 500 nM.
Gene expression data of the 197 BCs and 4 normal breast (NB) samples, which represented 1 pool of 4 samples from 4 women, and 3 commercial pools of respectively 1, 2 and 4 normal breast RNA (Clontech, Palo Alto, CA), were quantified using whole-genome DNA microarrays (HG-U133 Plus 2.0, Affymetrix).
Gene expression levels at all three stages were quantified using the PN40024 genome and the Corvina private genes as reference sequences.
Viral genome of extracted DNA and some cDNA samples were quantified using limiting dilution PCR [26], [27].
The normalised samples were quantified using Qubit and three from each genome were selected for library construction.
The probe set intensities were quantified using the Affymetrix Scanners using GeneChip Command Console (AGCC) and analyzed with RMA normalization using Genome Console software (Affymetrix).
Immunoblots were quantified using ImageJ.
RNA samples were quantified using spectrophotometry.
Proteins were quantified using Bradford protein assay.
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