MOESM1 of Continued in vitro cefazolin susceptibility in methicillin-susceptible Staphylococcus aureus

Additional file 1: Figure S1. Quality control performances of weekly cefoxitin, cefazolin, and ceftriaxone disk diffusion the study period. Figure S2. Post hoc measurement of zones of inhibition generated from ceftriaxone and cefazolin disks against clinical isolates (n = 153) of MSSA. Heterogeneous or “beach”-type of zone phenotypes around ceftriaxone disk could be sized typically by either at ~ 80% growth inhibition or at the complete growth inhibition (Note: The measurement at the complete growth inhibition has been the standard for susceptibility interpretations). Insert graph shows “cliff”-type of homogeneous zone measurements around cefazolin disk

Additional file 1: Table S1. of Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

Optimization of word count for MegaBLAST alignment to the NT reference database. (XLSX 12 kb

Additional file 2: Table S2. of Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

MetaPORE performance according to system configuration and alignment mode. (XLSX 18 kb

Additional file 5: of Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6

Figure S4. Gel image of silver stain of HHV-6B Z29 lysate in SupT1 cells or serum-free supernatant run on 4-12% TrisHCl gel in MES buffer. (PDF 1335 kb

Additional file 4: of Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6

Figure S3. Non-contiguous gel images of silver stain of HHV-6B Z29 lysates in SupT1 cells or serum-free supernatant run on 10-20% TrisHCl gels in MOPS buffer. (PDF 3011 kb

Additional file 8: of Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6

Table S4. HHV-6 Peptides Identified by Shotgun Proteomics. Mass spectrometry database search results are shown for HHV6 peptides identified using Protein Prospector v 5.19.1 described in Materials and Methods. The table reports the best matched peptide spectra. Provided are the mass to charge ratio (m/z), charge (z), mass error in ppm, the peptide sequence with previous and next amino acids in the sequence, variable modification, the fraction and retention time as spectrum identifiers. The start and end sequence numbers are given, along with Protein Prospector peptide score and peptide expectation value. (XLSX 88 kb

Additional file 3: of Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6

Figure S2. Phylogenetic tree of HHV-6B complete U90/91 and U94/100 loci. HHV-6B genomes were aligned using MAFFT, curated for sequence outside of repeat regions, and phylogenetic trees were constructed using MrBayes along the 6 kb U90/91 (A), and 10 kb U94-100 (B) regions. HHV6-6B NY310 was used as an outgroup. Samples are colored and labeled for origin based on New York (green), Japan (blue), or iciHHV6-B from HSCT recipients or their donors in Seattle (black), as well as whether two genomes were recovered from first-degree relatives (red). Location images purchased from Adobe Stock. (ZIP 656 kb

Additional file 1: of Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6

Table S1. List of samples sequenced in this study and associated accession numbers. (DOCX 72 kb

Additional file 6: of Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6

Table S2. RPKM values for RNA-Seq data. (XLSX 51 kb

Additional file 7: of Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6

Table S3. HHV-6 Proteins Identified by Shotgun Proteomics. Mass spectrometry database search results are shown for HHV6 proteins identified using Protein Prospector v 5.19.1 as described in Methods. Data were scored at the 5% FDR with Protein and Peptide minimum scores of 22 and 15, and maximum expectation values for proteins and peptides of 0.01 and 0.001, respectively. The number of unique peptides, the peptide (or spectral) count, the percent sequence coverage and the best peptide expectation value are given for each protein identification, merged from all samples. (XLSX 53 kb