Restriction enzyme digestion software
Samples were then processed as described above by restriction digestion, PCR enrichment, and deep sequencing. Each digested sample was paired with an identical sample that was not restriction digested. The resulting sequencing reads were mapped against the reference database for quantification of parasite-derived reads.
Note that for every experiment, an unquantified proportion of human reads was contributed by human products in the P. For analysis of assay limit of detection, frozen samples of P. Samples were processed and sequenced as described above, in triplicate, with restriction digested samples paired with an identical undigested sample sequenced on the same run.
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Sci Rep. Efficient depletion of host DNA contamination in malaria clinical sequencing. J Clin Microbiol. Toxoplasma gondii and Cryptosporidium parvum lack detectable DNA cytosine methylation. Eukaryot Cell. Mol Biochem Parasitol. Rojas MV, Galanti N.
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BioMed Central Ltd. Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification. Malar J. BioMed Central. Selective whole-genome amplification is a robust method that enables scalable whole-genome sequencing of Plasmodium vivax from unprocessed clinical samples.
Am Soc Microbiol. Google Scholar. Human gut microbiome viewed across age and geography. Characterization of the gut microbiome using 16S or shotgun metagenomics. Front Microbiol. Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome.
Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing. Deep sequencing of the 16S ribosomal RNA of the neonatal oral microbiome: a comparison of breast-fed and formula-fed infants. Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data. BMC Bioinformatics. Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Res. Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing.
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Download references. We also gratefully acknowledge Samuel Thaseal for discussions and helpful suggestions. The materials analyzed during the current study will be made available from the corresponding author on reasonable request. Briana R. Flaherty, Joel Barratt, Kristine J.
IHRC, Inc. You can also search for this author in PubMed Google Scholar. BRF optimized the experimental design, performed the majority of experiments, analyzed the data, and generated the figures. ET conceived the method, developed the experimental design, and assisted with data analysis.
JB designed the dual-criterion test for positivity and assisted with data analysis and editing of the manuscript. CO assisted with conception of the method and data analysis.
ML assisted with LOD and mock digestion experiments. RSB conceived the project, obtained funding, supervised the study, and assisted with conception of the method and experimental design. All authors read and approved the final manuscript.
Correspondence to Richard S. Ethics approval for the use of anonymized, de-identified, non-reidentifiable blood samples as non-engaged research was granted by Centers for Disease Control and Prevention Division of Parasitic Diseases and Malaria Human Subjects Review, approval number The authors declare that they have no competing interests. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Figure S1. TIF kb. Figure S2. Plots demonstrate a shift in reads for all parasite species tested: a P. Figure S3. Skewed results for W. Uneven distribution of microfilariae in the clotted samples led to variations in parasite DNA concentrations in each aliquot and inconsistent resultant reads a. Nevertheless, reductions in human reads per thousand were consistent with other analyses at 1. Meanwhile, L. Because of the lack of human DNA background, L. Data shown represents results for 3 biological replicate runs.
Figure S4. Mock digestion of human blood spiked with cultured 3D7 P. Figure S5. Differences in sequence are shown in color. Table S1. Common name, scientific name and Genbank accession number of vertebrates tested in silico and found to be suitable candidates for host reduction by this universal blood parasite detection method. Careful planning, dedicated researchers, and the right tools. At Takara Bio, we thoughtfully develop best-in-class products to tackle your most challenging research problems, and have an expert team of technical support professionals to help you along the way, all at superior value.
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Our mission is to develop high-quality innovative tools and services to accelerate discovery. We use cookies to improve your browsing experience and provide meaningful content. Read our cookie policy. Restriction enzyme overview. Find a restriction enzyme. Traditional molecular cloning Restriction enzyme overview General information about restriction enzymes Star activity of restriction enzymes Inactivation of restriction enzymes Buffer activity with restriction enzymes Universal buffers for double digestion with restriction enzymes Restriction enzymes affected by methylation Methylation-sensitive restriction enzymes QC of restriction enzymes Ligation cloning overview Ligation product guide.
New products. Contact Sales. Universal buffers for double digestion with restriction enzymes Double digestion digesting DNA with two restriction enzymes simultaneously is frequently performed to save time.
To specify a restriction digest, choose cut with default from the menu. Specify the Restriction Enzymes. The restriction digest will be automatically simulated.
Apply to All Lanes. View the Simulated Agarose Gel. The simulated agarose gel for the restriction digest will be shown. Rapidly Simulate a Restriction Digest. Repeat this step to populate other lanes.
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