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Quantitating primer-template interactions using a deconstructed PCR methodology

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Quantitating primer-template interactions using a deconstructed PCR methodology https://t.co/BxSwebHkMA https://t.co/NFjEutcGBJ
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Supplemental Information

Template and primer utilization profiles for 16 individual experiments conducted in this study

For each study, varying number of primers and templates were used, as described in Table 1. For mMDS plots, samples were color coded by amplification method and different annealing temperatures indicated by shape. Ellipses represent a 95% confidence interval around the centroid. ANOVA was performed to measure differences in measured values by annealing temperature. Intensity scales vary between experiments. All samples were rarefied to 7,000 sequences. Heatmaps are the average of 7-8 technical replicates per condition; all replicates are shown in mMDS plots. (A) For each experiment, primer utilization profiles (PUPs) were generated (left side), and data are presented as mMDS plots (top) and as clustered heatmaps (bottom). Analysis of similarity (ANOSIM) was performed to determine if PUPs were significantly different between TAS and DePCR, regardless of annealing temperature, and within method across annealing temperature. Each slide contains a table showing the percentage of reads with 0, 1, 2 and 3 mismatches between primers and templates, as indicated in experiments with DePCR amplifications. For primer-template interactions with only a single mismatch, percentage of reads with 3’ (-2), middle (-8) and 5’ (-14) mismatches are shown. The average theoretical melting temperature of primers used in each study are shown. (B) Template profiling analyses were performed (right side), and data are presented as mMDS plots (top) and as clustered heatmaps (bottom). In addition to analysis of sequence data, the expected distribution of reads is shown in orange, both in the mMDS plots and in the heatmap. ANOSIM was performed to determine if template profiles were significantly different between TAS and DePCR, regardless of annealing temperature, and within method across annealing temperature. Ideal scores, as described in text, were calculated to determine which method and annealing temperature generated the closest approximation of the expected template distribution.

DOI: 10.7287/peerj.preprints.27781v1/supp-1

Effect of PCR methodology and annealing temperature on template profiles in amplification reactions utilizing varying primer pools

One-way clustered heatmaps of untransformed template utilization profiling during amplification of an uneven pooling of synthetic DNA templates and varying primer pools (Figure S17 = C1, C2 and C3 experiments with all ten templates present, and template ST1 at 1/10th the concentration of the other nine templates; Figure S18 = D1, D2, E1 and E2 experiments with four templates). For experiments C1, D1 and E1, only a single primer variant was used (806F_v1), while in experiments C2, D2 and E2, 10 primers were used. In experiment C3, 9 primers were used (806F_v1 was removed). Primer and template details are shown in Table 1. Samples (columns) are color-coded by amplification method (TAS or DePCR), amplification annealing temperature (45°C or 55°C), and average Ideal score. Each column represents the average of 7-8 technical replicates per condition and rarefaction to 7,000 sequences/replicate. Templates (rows) represent all 10 templates (ordered from top to bottom; ST1, ST4, ST6, ST7, ST8, ST11, ST15, ST23, ST39, and ST55). Ideal score comparisons between TAS and DePCR (across both annealing temperatures), within TAS (45°C or 55°C), and within DePCR (45°C or 55°C) are shown in tables. Asterisks indicate significant differences in measured values by annealing temperature (ANOVA, P < 0.01). Intensity scales vary between experiments.

DOI: 10.7287/peerj.preprints.27781v1/supp-2

Locus-specific primer sequences used in this study

For each primer, the locus-specific sequence is shown (column B) and a 5' linker sequence (column F) are used. The combined primer sequence used in this study is shown as well (column G). Primer length, estimated melting temperature (Tm; calculated as described in the main text) and mismatches relative to the first 806 primer, 806F_v1, are shown.

DOI: 10.7287/peerj.preprints.27781v1/supp-3

Distribution of mismatches between primers and templates used in this study

Locus-specific primer names and primer sequences (columns A and B) are shown next to variant position sequences (column C). Columns F-O represent each of the 10 synthetic DNA templates used in this study, with nucleotide sequences at each potential mismatch position shown in rows 3 and 4. Number of mismatches between templates and primers are colored in columns F-O and rows 5-68. Columns Q-U indicate which primers are used in which series of experiments (1-6). Rows 70-74 indicate which templates are used in which series of experiments (A-E), and are shaded according to relative concentration of each template in each template pool.

DOI: 10.7287/peerj.preprints.27781v1/supp-4

Rarefied biological observation matrix (BIOM) for all experiments

Data were rarefied to 7,000 sequences per sample, and each experimental condition has 7-8 replicates. A total of 640 possible interactions are listed (10 templates x 64 primers), and numbers represent the numbers of reads matching each of the combinations. For each row of the BIOM, the number of mismatches between primer and template are shown, along with the position of mismatch, the mismatch sequence pairing, and the theoretical melting temperature of the primer. Reactions conducted with DePCR are highlighted in blue; no highlighting is used for TAS amplification reactions.

DOI: 10.7287/peerj.preprints.27781v1/supp-5

Mapping file used for creation of biological observation matrices (BIOMs)

This mapping files is used by the script described in the text and provided in Supplemental Materials 2.

DOI: 10.7287/peerj.preprints.27781v1/supp-6

Metadata associated with all samples used in this study

Metadata for each replicate is shown, including the number of raw sequence reads, processed reads, calculated Shannon Index (loge), Ideal Score (calculated as described in the text), and figure(s) where data are shown.

DOI: 10.7287/peerj.preprints.27781v1/supp-7

Description of synthetic DNA template design and template sequences

Ten DNA templates were synthesized for this study, and the backbone of the template was derived from the 16S rRNA gene of the bacterium Rhodanobacter denitrificans 2APBS1. The source sequence is shown, along with its inverse complement and region used for gBLOCK synthesis. The design strategy for each gBLOCK is also provided in greater detail. Finally, the exact sequences used for synthesis of each of the templates is shown with primer sites and recognition sequences highlighted.

DOI: 10.7287/peerj.preprints.27781v1/supp-8

Script used for generation of BIOM files

DOI: 10.7287/peerj.preprints.27781v1/supp-9

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Ankur Naqib conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Trisha Jeon performed the experiments, approved the final draft.

Stefan J Green conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

Raw sequence data files were submitted in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI). The BioProject identifier of the samples is PRJNA513137. Full metadata for each sample are provided in Table S5.

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA513137

Data Deposition

The following information was supplied regarding data availability:

Data is available at NCBI SRA, BioProject identifier PRJNA513137.

A small script was generated for this study as well, and this is provided as a Supplemental Materials document.

Funding

The authors received no funding for this work.


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