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Additional file 2: Table S2. Prevalence of classified genera in datasets processed by Qiime1 and Qiime2 after excluding OTUs/ASVs with less than 20 reads across each dataset. Table S4. Prevalence of classified genera in datasets processed by Qiime1 and Qiime2 after excluding OTUs/ASVs with less than 20 reads across each dataset and mean relative abundance of less than 0.01%.

Additional file 5: Table S4. EGFR information on LGSC cell lines.

Table S1A. All hydrogen deuterium exchange (HDX) peptide data for experiments examining the global exchange of PI4KIIIA, TTC7B, and FAM126A. The charge state (Z), residue start, residue end number, retention time (RT) and sequence are displayed for every peptide. In the Raw Data column, the two time points (0.3s and full) are labelled, and the relative level of HDX is coloured according to the amount of deuterium incorporated, on a blue to red continuum. The data listed for the 0.3s time point are the average of three independent experiments, with SD shown next to all HDX values. In the Normalized to Full Deuteration column, the 0.3s data has been normalised to the full deuteration measurements with the exception of those data (surrounded by black lines) where the full deuteration measurement was lower than 20% deuterium incorporation. The third column denotes the corresponding peptide centroid. Table S1B. All HDX peptide data for experiments examining the complex dynamics of PI4KIIIA, TTC7B, and FAM126A. The charge state (Z), residue start, residue end number, retention time (RT) and sequence are displayed for every peptide. The two columns represent each state examined (+/- PI4KIIIA) and contain the data for five time points. The data listed are the average of three independent experiments, with SD shown next to all HDX values. Table S1C. All HDX peptide data for experiments examining the dynamics of inhibitor specificity of PI4KIIIA, TTC7B, and FAM126A. The charge state (Z), residue start, residue end number, retention time (RT) and sequence are displayed for every peptide. The three columns represent each state examined (+/- inhibitor) and contain the data for four time points. The data listed are the average of three independent experiments, with SD shown next to all HDX values.

Additional file 4: Table S3. A. Results for 34 independent ARIC Discovery Meta-Analysis identified mtDNA-CN associated CpGs across all studied cohorts and Validation Meta-Analysis/All Cohort Meta-Analysis. Validation meta-analysis included CHS AA, CHS EA and FHS EA cohorts (P < 0.05 and same direction, bolded cells). All cohort meta-analysis (ARIC AA, ARIC EA, CHS AA, CHS EA and FHS EA) identified 6 validated CpGs (P < 5 × 10–8, shaded cells). B. Results for 23 independent ARIC AA identified CpGs across all studied cohorts. C. Results for 15 independent ARIC EA identified CpGs across all studied cohorts.

Genome-wide predictions of cis-regulatory regions for all six cell types. (ZIP 20400 kb)

Overview of genomic instability of individual chromosome arms in both TCGA and CPC-GENE datasets. Genomic instability was calculated based on a modified PGA formula (see methods). P-values are based on a Wilcon–Mann–Whitney test while log2FC represents the log2 ratio of the average PGA scores for CR/IDC positive samples and CR/IDC negative samples. PGA scores for deletions and amplifications were calculated and tested separately. (XLS 139 kb)

Peptides from a CNBr digest of signal-sequenceless maltose binding protein (MBP) were coupled to a surface plasmon resonance (SPR) chip. SecA-N95, SecA-N68, and SecA-DM (which consists of only the DEAD Motor domains, NBD1 and NBD2) bound to the immobilized peptides; ADP weakened the binding. SecA-DM, which lacks the “preprotein cross-linking domain” (PPXD), displayed the most extensive binding, while an MBP-PPXD chimera showed no binding, demonstrating that the PPXD does not contribute to the binding. The sequence specificity was characterized using oriented peptide libraries; these results enabled synthesis of a 20-residue peptide that was used to recapitulate the results obtained with MBP-derived peptides. The study shows there is a promiscuous and nucleotide-modulated peptide-binding site in the DEAD Motor domains of SecA.

Additional file 6. Autocorrelation z scores between pairs of stimulated and unstimulated chromatograms.