318v2 chip

Extracted DNA underwent the process of amplicon library preparation using Ion 16STM Metagenomics Kit (Life Technologies, Carlsbad, CA, USA) following manufacturer instructions. Two sets of primers for the amplification of bacterial 16S rRNA were used: the first primer set was used to amplify 16S rRNA variable regions 2–4–8 (V 2–4–8), whereas the second primer set targeted 16S rRNA variable regions 3–6 and 7–9 (V 3–6; V 7–9). Prior to sequencing, the obtained amplicons of both primer sets were combined together for each sample. Immediately after preparation, libraries were examined for size, quality and concentration using Agilent High-Sensitivity DNA Kit and Bioanalyser 2100 instrument (Agilent Technologies, Santa Clara, CA, USA).
16S rRNA amplicon sequencing was performed using the Ion PGM System and 318 v2 chip (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer instructions.
To control laboratory contamination, tick 16S rRNA amplicon sequencing procedures were accompanied by corresponding blank samples, which were also treated equally and underwent the same library preparation steps. However, blank control samples showed no detectable amplification (Supplementary Figure S2).
Raw sequencing reads have been submitted to the European Nucleotide Archive, project accession PRJEB63277.

Barcoded semi-conductor sequencing analysis was performed essentially as described previously (27 (link)). Briefly, the 16S rRNA V5–V6 region sequences were amplified from 2 to 4 ng of DNA from each sample by PCR using the primers 799f and 1115r (27 (link)). The PCR amplicons were purified using E-gel Size Select 2% (Thermo Fisher Scientific) and Agencourt AMPure XP magnetic beads (Beckman Coulter, Brea, CA). After measuring DNA concentration using the Ion library quantification kit (Thermo Fisher Scientific), equal quantities of tagged amplicons were pooled. The pooled DNA samples (5 pM per sample) were then subjected to the Ion Chef and Ion PGM (400 bases) sequencing platform using a 318v2 chip (Thermo Fisher Scientific), according to the manufacturer's instructions.

Panel-based next-generation sequencing was performed following the manufacturer's instructions. Briefly, 10 ng of genomic DNA were used for preparation of barcoded PCR-libraries using the comprehensive cancer panel. Libraries (100 pM of each primer pool per cell line) were mixed, amplified and bead-coupled by emulsion PCR using the OneTouch 2 system. Sequencing of duplexed samples was performed on the Ion Personal Genome Machine (PGM) System and a 318v2 chip (all equipment from Thermo Fisher Scientific, Waltham, MA, USA). Variant call files were analyzed by our in-house pipeline and mutations were selected regarding prediction of potential impact on protein function by algorithms SIFT/PolyPhen^{54 (link), 55} and MutationTaster.^{56 (link)} Analysis of CNV was performed with R package CNVPanelizer using BAM/BAI sequencing output files. Determination of CNVs of resistant MeWo cells was referenced to sensitive (MeWo^Par) cells.