Visitors   Views   Downloads
NOT PEER-REVIEWED
"PeerJ Preprints" is a venue for early communication or feedback before peer review. Data may be preliminary.

Supplemental Information

Location of MTBC primer-probes on the insertional elements, IS1081 and IS6110

The location of primer-probe sets for Mycobacterium tuberculosis complex insertional elements A) IS1081. B) IS6110. Primers designated “Miller” refer to Miller et al. 1997.

DOI: 10.7287/peerj.preprints.1703v1/supp-1

Primers and probes

Primers and probes used for real-time PCR identification of M. tuberculosis complex and M. bovis.

DOI: 10.7287/peerj.preprints.1703v1/supp-2

Initial performance of the primer and probe sets

The initial performance of the selected primer and probes designed to detect M. tuberculosis complex and M. bovis. A) Analytical sensitivity using M. bovis DNA. B) Calculated slope, R2 value, efficiency, and lowest detectable DNA concentration for each primer-probe set

DOI: 10.7287/peerj.preprints.1703v1/supp-3

Comparison of 3 DNA isolation methods using purification method A (magnetic bead) or method B (spin column)

Three DNA isolation methods, NaOH, phenol/chloroform and TE were evaluated using 3 replicates of 5 different samples. If all 3 replicates signaled positive, a mean and standard deviation of the Cτ were calculated. All 3 isolation methods were compared using 2 DNA purification methods; method A (magnetic bead) or method B (spin column).

DOI: 10.7287/peerj.preprints.1703v1/supp-4

Comparing DNA isolation and purification methods

Estimates and 95% confidence intervals comparing differences in means of two DNA isolation methods and two DNA purification methods. Using a linear model, the means differences in Cτ values per sample were generated and a 95% confidence interval calculated for each comparison. A result was considered statistically significant if the 95% CI did not span zero. A, B: Comparison of DNA Isolation methods using either DNA Purification method A or B. C, D: Comparison of DNA Purification Methods A and B using either DNA Isolation method 2 or 3.

DOI: 10.7287/peerj.preprints.1703v1/supp-5

Comparison of extraction method 2 and 4

DOI: 10.7287/peerj.preprints.1703v1/supp-6

Archived tissue sample test results used to evaluate sensitivity

DOI: 10.7287/peerj.preprints.1703v1/supp-7

Slaughter surveillance, side by side testing with PCR and the traditional histology and culture workflow

DOI: 10.7287/peerj.preprints.1703v1/supp-8

Post validation slaughter surveillance IS1081-3 PCR dataset

DOI: 10.7287/peerj.preprints.1703v1/supp-9

PCR results from known infected herd samples using the IS1081-3 and the L3 primer-probe sets

DOI: 10.7287/peerj.preprints.1703v1/supp-10

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Philip E Dykema conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Kevin D Stokes conceived and designed the experiments, analyzed the data, prepared figures and/or tables, reviewed drafts of the paper.

Nadine R Beckwith performed the experiments, reviewed drafts of the paper.

James W Mungin performed the experiments, reviewed drafts of the paper.

Lizhe Xu conceived and designed the experiments, reviewed drafts of the paper.

Deborah J Vickers performed the experiments, reviewed drafts of the paper.

Monica M Reising conceived and designed the experiments, analyzed the data, reviewed drafts of the paper.

Doris M Bravo performed the experiments, reviewed drafts of the paper.

Bruce V Thomsen performed the experiments, reviewed drafts of the paper.

Suelee Robbe-Austerman conceived and designed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

All raw data was uploaded along with the paper as supplemental files.

Funding

The funding for this research was provided by the United States Department of Agriculture as appropriated funds for the State Federal Cooperative Bovine Tuberculosis Eradication Program. The Thurgood Marshall College Fund partially funded JWM as a summer intern. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


Add your feedback

Before adding feedback, consider if it can be asked as a question instead, and if so then use the Question tab. Pointing out typos is fine, but authors are encouraged to accept only substantially helpful feedback.

Some Markdown syntax is allowed: _italic_ **bold** ^superscript^ ~subscript~ %%blockquote%% [link text](link URL)
 
By posting this you agree to PeerJ's commenting policies