Interrogation of the Breast Invasive Carcinoma (TCGA, Cell 2015 24 which contains 1,105 samples was performed using cBioPortal.
The analysis of samples was performed using HPLC instrument (Agilent) equipped with a Rezex RPM-Monosaccharide Pb2+ column (300 × 7.8 mm; particle size 8 μm) at 80 °C.
The characterization of the samples was performed using nuclear reaction analysis and Rutherford backscattering spectroscopy.
A complete morphological characterization of the samples was performed using XRD, TEM, SEM, N2 adsorption and surface hydrophilicity measurements.
A blinded study of 163 samples was performed using this new assay and it was concordant with the original methods.
The two-groups comparison, each group consisting of n = 4 independent samples, was performed using the genewise negative binomial generalized linear model with quasi-likelihood tests (glmQLfit) implemented in EdgeR.
Assessment of pathway activity in single AML samples was performed using a single-sample gene set enrichment method which aggregates z-score transformed gene expression values of a given gene set into a single pathway activity score34.
Taxonomic profiling of the metagenomic samples was performed using MetaPhlAn220, which uses a library of clade-specific markers to provide panmicrobial (bacterial, archaeal, viral, and eukaryotic) profiling (http://huttenhower.sph.harvard.edu/metaphlan2).edu/metaphlan2
Transmission electron microscopy (TEM) of SiO2 samples was performed using a JEOL-JEM microscope model 2100.
An assessment of form change in pre- and post-milling samples was performed using PXRD.
The method used for detection of yeast and fungi in samples was performed using dilution plating method.
