Selection of samples from 2008/2009 for this assay was based on availability of samples with enough volume.
The biomarkers were initially selected based on a thorough search of the current diabetes biomarker literature, narrowed based on the availability of assay reagents that could be incorporated with high quality into the assay system, and then further selected using statistical modeling.
HTS data were collected for 10 out of the 48 human NR, selected based on availability of assays and potential relevance to toxicology, including: members of the NR1, NR2, NR3 and NR4 subfamilies.
The dataset of overlapping genes was also analyzed based on availability or non-availability of EST evidence.
The number of samples included in each assay varied based on the availability of cells at the time of testing.
Samples from baseline (n = 24), 1 month (n = 30), 3 months (n = 33), 9 months (n = 60), and 15 months (n = 44) were included in the assay based on availability.
Cell lines were selected primarily based on the availability of publicly available expression data, availability for commercial purchase, and the compatibility with use in an in vitro chemosensitivity assay.
25 proteins were chosen based on availability of ELISA assays.
Selection was based on the availability of sufficient serum for repeat assays and the known presence of anti-GAD65 in the serum.
To verify the differential abundance observed by mass spectrometry, ELISA assays were performed on selected proteins based on commercial availability (Pf4, Igf1, Igfbp5, and Lcn2) (Figure 4).
