The outside bar looked ill-defined, the swell confused, but the outside waves themselves were smooth and shiny, with clean peaks and sections looming randomly in the mist.
This is demonstrated in Figure S2D where clean peaks for 18S and 28S rRNA are still evident after fixation, staining, and sorting.
A window around each artifact is removed and the entire filtered, cleaned dataset is fit with a spline such that clean peaks are modeled and the windowed gaps are replaced with values from the spline interpolation to produce a clean, spline waveform (Figure 2).
Well resolved and clean peaks were reintegrated and fold changes were recalculated manually.
While many genes have very clean peaks corresponding to the exons (Additional file 1: Figure S2), we find that long genes with high expression levels show a surprisingly high intron read coverage in nuclear, total and polyA+ RNA.
After baseline subtraction, clean Mn peak amplitudes were measured to plot the calibration curve and to calculate detection limit.
Sequences were considered heterozygous when at least one clean chromatogram peak supported only the alternate allele or at least two were heterozygous (as determined by eye).
When 11 is exposed to a control E. coli cell lysate, Nimzyme reveals a clean mass peak corresponding to this substrate (Fig. 2d).
Standard curves were performed for all primers prior to analysis and melting curves were analyzed for clean single peaks.
