Additional file 1: Figure S1. of Respiratory microbes present in the nasopharynx of children hospitalised with suspected pulmonary tuberculosis in Cape Town, South Africa

Seasonal distribution of viruses and bacteria. Figure S2. Canonical Variate Analysis (CVA) biplot depicting the spread of respiratory pathogens in the definite TB (red line) and not TB (blue line) groups only. Observations under each group are denoted by “+” signs and the median of each group by the red and blue ovals. Table S1. Target pathogens in the FTD respiratory pathogens 33 multiplex realtime PCR assay. Table S2. Summary of all paired pathogen co-occurrence counts *. Table S3. Risk factors associated with the occurrence of each microbes. (PDF 565 kb

Additional file 1: of Maternal blood contamination of collected cord blood can be identified using DNA methylation at three CpGs

Table 1. Primer sequences used for pyrosequencing. Table 2. Beta value thresholds used for DNA methylation arrays and pyrosequencing. Figure S1. Strategy used to identify contamination in male samples. Plotting PC2, which separated male from female samples in our data, against DNA methylation at a CpG in XIST on the X chromosome, revealed three populations of male samples: contaminated, non-contaminated, and a group of five samples which were unclear. Figure S2. Neither epigenetic age (A), gestational epigenetic age (B) nor number of genotyping “no calls” (C) were sufficient to identify maternal blood contamination of cord blood. In all cases, contaminated and non-contaminated males showed high overlap, indicating insufficient discrimination. Figure S3. Across-batch differences in DNA methylation level support the use of multiple predictive CpGs for identification of contamination. Residual plot of discovery data (A), validation data (B), publically-available data (C), and PREDO (D) indicate technical spread across samples and studies. In particular, EPIC data (second cohort, top right) shows greater variability and higher baseline levels than the 450K data sets. (PDF 759 kb