Additional file 1: of A novel enrichment strategy reveals unprecedented number of novel transcription start sites at single base resolution in a model prokaryote and the gut microbiome

Supplement. Contains all Supplementary Notes and Supplementary Figures and Table S2. (GTF 2008 kb

Additional file 2: of A novel enrichment strategy reveals unprecedented number of novel transcription start sites at single base resolution in a model prokaryote and the gut microbiome

contains Table S1. (ZIP 9431 kb

Application of EcoWI-seq analysis with <i>de novo</i> assembly.

(A) Features of de novo assembly using SPAdes assembler. (B) Table listing numbers and overlapping of called modified sites between de novo assembly and using reference genome. (TIF)</p

Genomic mapping of PT modification at single base resolution by EcoWI-seq.

(A) Motif logo of positions with more than 50 5’ end reads in the genome of WT Dnd+ SenC87 strain. (B) Plots of modification scores in the genome of WT Dnd+ (top) and ΔdndE mutant (bottom) strains. Dashed line showed the modification score cut-off used to call PT-modified sites. (C) Numbers of identified PT-modified sites by category.</p

PT modified positions called by EcoWI-seq analysis in WT <i>Sen</i>C87.

This file can be open using any free text editors. (SITES)</p

Investigation of target modification sites in <i>E</i>. <i>coli</i> heterologous PT modifying system.

(A) Experiment design. Stars represent PT modifications in the genome. (B) Correlations among the 6 SenC87 dnd/pBC4 transformed E.coli strains. For each pair of comparisons, modification scores of all possible GAAC/GTTC sites were used for correlation calculation. Color bar on the side indicated the Pearson correlation values. For SenC87 dnd transformed E. coli strains, correlations were also performed among the technical duplicates (rep1 and rep2). (C) Output of Two Sample Logo [31]: Graphical representation showing statistically significant (p value E. coli.</p

Genomic mapping of PT modification at single base resolution by EcoWI-seq.

(A) Frequencies of modification level at all possible GAAC/GTTC sites for WT Dnd+ (orange) and ΔdndE mutant (blue) SenC87 strains. (B) Curve showing the number of PT modified sites identified at different modification score cutoff. The cutoff for calling modified sites in this experiment was determined by visual observation of the deviation from the tangent point. (value = 20). (C) Scatter plot showing correlation of modification scores in two independent replicates. Each dot represents a GAAC/GTTC site. (D) Motif logo of the flanking regions of non-canonical GAAC/GTTC sites. Positions are relative to the predicted cutting site (position 0). (E) EcoWI digestion of PT-modified duplex oligos containing GpsTAC or unmodified GTAC site. S, P1, and P2 refer to substrate (58mer), cleavage products 1 and 2, respectively. EcoWI digest condition, PAGE analysis, DNA fragment staining and imaging were described in the Materials and Method. EcoRI-HF (RI) was used as a positive control for restriction. (TIF)</p

Bacteria strains containing PT modification and their corresponding PT-modified consensus motifs.

This is a.CSV file that can be open in any free text editors or Microsoft office. (CSV)</p

Kinetic signals from SMRT sequencing at modified bases.

(GFF)</p

Establishment of PT modification system in heterologous host <i>E</i>. <i>coli</i>.

(A) Plots of modification scores in the genome of SenC87 dnd transformed and pBC4 transformed E. coli strains. Dashed line showed the modification score cutoff used to call PT modified sites. (B) Numbers of identified PT-modified sites by category. (C) Output of Two Sample Logo: Graphical representation showing statistically significant (p value SenC87 genome. (TIF)</p