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Comparisons of CMT-scores between quarters with different bacterial findings were performed using the Chi-square test.
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Initial gene finding was performed using GeneMarkS [ 31, 32].
Protein-coding gene finding was performed using three programmes: GeneMarkS, MetaGeneAnnotator, and GLIMMER3.
Cone finding was performed using a Bayesian approach described previously (Field et al., 2010).
The de novo motif finding was performed using i-CisTarget [ 37].
Grids were manually placed and spot finding was performed using the 'Auto adjust' spot function repeated three times.
ChIP-seq reads were mapped to hg19 with Bowtie, and peak finding was performed using sissrs [ 21].
Peak finding was performed using a Model-based Analysis of ChIP-Seq (MACS, version 1.3.7.1 - Oktoberfest) algorithm [ 46].
In order to shed light into the experimental findings, theoretical calculations were performed using two examples of filled and unfilled achiral MWCNTs and the results for the density of electronic states indicate that the two systems under consideration, exhibit metallic behavior, with aluminum carbide doping the carbon nanotubes, thereby supporting our experimental observations.
After imaging, spot-finding and quantification were performed using Dapple software [ 64].
To extend these findings, in vivo studies were performed using SK-Hep-1 and HepG2 xenograft tumor-bearing mice.
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