Notice that the same parameter values were used in all experiments described below, unless clearly stated otherwise for particular experiments.
In our image setting, the voxel intensities often fluctuate throughout the slice sequence of a -stack, probably due to the setup and chosen parameters of the imaging facility for particular experiments.
Expression profiles for the SRF genes are shown in Figure 8. SRF gene expression is present over a wide range of experiments and most of them show, at least for particular experiments, specific profiles.
For particular experiments, folate-depleted cells were washed in folate-free media, and cultured in complete folate-free RPMI 1640 without nucleosides and in the presence of LCV (0.5 200 nM).
For particular experiments that contain only two groups of samples, such as normal state versus disease state and tumour adjacent tissue versus primary tumour tissue, we conducted differentially expressed gene analysis.
Since the absence of Xrn1 leads to the accumulation of decapped RNAs (Hsu and Stevens, 1993), we could not use the TSS sequencing methodology applied for the other mutants and we thus used, for this particular experiment, a classical RNA sequencing approach for transcript quantification (see 'Materials and methods').
Generally, the number of ions monitored by the instrument in MIM mode should be set as low as possible (up to 10), but sufficient for any particular experiment, as they compete for quadrupole time in a measurement cycle.
For this particular experiment, we designed specific primers for four selected genes (see Methods), including one house-keeping gene encoding tubulin A6 (NtTUBand and three selected genes coding for a homologue of At4g24110, a metallophosphatase, and a virus resistance (N) gene.
For this particular experiment, we used the silica substrates (later, for demonstration purposes in the "Discussion" section, also silicon and oxidized silicon substrates were also used).
In most cases we are not told why a given driver line was selected for a particular experiment or, importantly, the normal expression pattern for each line with respect to LALv1 and ALad1 and other lineages with which they might be confused.
Experimental results were consistently observed in cells from six or more animals, hence all the results for a particular experiment were pooled and displayed as means±S.E.M save for the firing rate histograms where histogram properties were reported as means±S.D.; groups were compared with Student's t test.
