The optimum that we observe might be explained by the existence, for each specific sample type, of a concentration threshold above which spermidine no longer blocks PCR inhibitors, may be due to steric effects or saturation, and starts massively binding to DNA, so inhibiting PCR.
In general, these procedures, like all wet digestions of organic matter, should be attempted only with small test portions of known material, strictly following well-established procedures designed for the specific sample type.
In order to standardize the study, we controlled for the variability of results by using one specific sample type; thus, deciduous mandibular incisors were excluded from the study.
The improvement methods described above might be an excellent approach for one analyte, detrimental to another, and only applicable to one specific sample type.
Figure 6 indicates the number of genes expressed in the test samples in a cell-type specific manner (ts-score >0.75) when compared against three specific sample types in the reference database (hematopoietic stem cells, granulocytes and monocytes).
A wide range of approaches that facilitate low abundance peptide detection have been investigated, with some techniques applicable to specific sample types (sample preparation16,17), while others are more broadly applicable (data acquisition7,10,18,19,20,21).
From the PCA results, the eigenvalue plot indicated that 10 principal components (PCs) could be used to describe 92% of the data variation, however the first 4 PCs showed specific sample types which tended to be distinct from the other samples.
Inhibitors of enzymatic reactions were detected at high frequency in specific sample types such as heparinized blood and bone marrow (>70%), broncho-alveolar liquid (41%) and stools (36%).
While there are hundreds of studies on the expression of individual kinase genes or proteins in specific sample types, this represents to our knowledge the first systematic attempt to compare mRNA expression levels across all kinases and across all major tissue and tumor types with similar methodology.
The basic principles of the methods described below are the same, while modifications thereof will be presented in the sections dedicated to specific sample types.
