Specifically, we utilized the STAR 2-pass method, described recently [ 72].
To measure the extent of MT attachment at the KT, we adapted the method described recently (Toso et al, 2009).
In addition, the antioxidative capacity of acetonitrile-deproteinized plasma samples was measured using the 2,2-diphenyl-1-picryl-hydrazyl (DPPH) method described recently (Chrzczanowicz et al., 2008).
The relative risk is an appropriate outcome in prospective studies, and we used a method described recently by Zou based on a modified Poisson regression, which also allowed for clustering of the data [ 15].
We employed (i) a statistical method described recently using B-score and Z-score normalization of intensity read-outs of segmented cell images (Brideau et al., 2003), (ii) intensity read-outs of a luciferase based secondary screen and (iii) our new application of the point pattern analysis method.
These genome-scale comparisons are becoming routine and the approaches can be divided into two main categories, alignment-based (for example, an alignment of about 400 universal proteins identified by Segata et al. 2013) and alignment-free (for example, the "google DNA" method described recently; Gautier and Lund 2013).
The analysis of plasma-glycerophospholipids composition was performed by a sensitive and precise high-throughput method as described recently [23].
Preparation of plasmid DNA was done by using a phenol/chloroform-based extraction method as described recently [ 52].
We also assessed in parallel the expression of presumptive miR-34-regulated target genes and proteins, using the primers and methods as we described recently [6].
Several methods have been described recently for discriminating between 5mC and 5hmC using bisulfite sequencing in combination with chemical or enzymatic conversion [ 14, 15].
