Fig. 4

Normalization reduces amplification bias. A NB normalization reduces amplification bias. Variation in ST counts within samples is apparent before normalization (red), however, the ST-to-ST differences within each sample are reduced to less than two-fold after normalization (cyan). Data derived from twenty ST-only samples described in the ST-only data sets. B Amplification bias of spleen genomic DNA of P14 and OT-1 TCR transgenic mice. To further evaluate normalization parameters, a 50:50 mixture of P14 and OT1 TCR transgenic monoclonal DNA was utilized to examine differences between transgenic TCR counts (red) that were reduced for all samples following normalization (cyan), as observed by the smaller deviations from ½ of the proportions of the dominant clonotype. Red color indicates values from clone counts before normalization, green color indicates values from normalized clone counts. Data derived from 12 50:50 mixture of P14 and OT-1 transgenic mice samples described in the Transgenic TCR data sets