urine cell free dna urine  (Streck Laboratories)

Journal: Scientific Reports

Article Title: Metagenomic DNA sequencing to quantify Mycobacterium tuberculosis DNA and diagnose tuberculosis

doi: 10.1038/s41598-022-21244-x

Figure Lengend Snippet: ( A ) The fragment length distributions of M. tuberculosis DNA in plasma (red) and urine (blue). ( B ) The fragment length distribution of M. tuberculosis DNA (purple) and host chromosomal DNA (green) in oral swabs are similar, suggesting that the microbial DNA is genomic and the fragmentation profile is not an intrinsic property but rather the consequence of sample preparation steps. ( C ) The abundance of M. tuberculosis DNA across all cohorts and biofluids. The majority of non-endemic samples have little to no detectable M. tuberculosis DNA, while the abundance of M. tuberculosis DNA in endemic and tuberculosis samples increases from plasma to oral swab. Dashed line indicates a limit of detection cutoff of 0.1 RPM.

Article Snippet: For the tuberculosis cohort, approximately 10 mL of urine was mixed with 2 mL Streck Cell-Free DNA Urine Preserve (Streck, Cat #230604) and centrifuged at 3000× g for 30 min at ambient temperature within 30 min of specimen collection.

Techniques: Sample Prep

Journal: Clinical Chemistry

Article Title: Measurement Biases Distort Cell-Free DNA Fragmentation Profiles and Define the Sensitivity of Metagenomic Cell-Free DNA Sequencing Assays

doi: 10.1093/clinchem/hvab142

Figure Lengend Snippet: Sensitivity of metagenomic cell-free DNA sequencing is a function of the choice of DNA isolation and library preparation methods. ( A) Fraction of microbial cfDNA (MPM) for 4 library preparation protocols relative to the CNA kit for cfDNA isolation. (B) Fraction of microbial cfDNA recovered (MPM) for two library preparation protocols relative to the Meyer protocol for library preparation. Blue diamonds indicate the expected MPM based on modeling.

Article Snippet: For the tuberculosis patient samples, 10 mL of urine was mixed with 2 mL Streck cell-free DNA urine preserve (Streck, USA) and centrifuged at 3000 g for 30 min at ambient temperature.

Techniques: DNA Sequencing, DNA Extraction, Isolation

Journal: Clinical Chemistry

Article Title: Measurement Biases Distort Cell-Free DNA Fragmentation Profiles and Define the Sensitivity of Metagenomic Cell-Free DNA Sequencing Assays

doi: 10.1093/clinchem/hvab142

Figure Lengend Snippet: Characterization of fragment length bias introduced by cfDNA sequencing assays. ( A) Synthetic cfDNA was prepared by mixing sheared ΦX174 DNA. (B) The fragment length distributions were measured before and after each assay step to obtain the efficiency of fragment recovery as a function of fragment length. The product of (C) cfDNA isolation, (D) library preparation, and (E) sequencing efficiencies was taken to be (F) the overall transfer function (shown for various isolation kits after library preparation with the Meyer protocol).

Article Snippet: For the tuberculosis patient samples, 10 mL of urine was mixed with 2 mL Streck cell-free DNA urine preserve (Streck, USA) and centrifuged at 3000 g for 30 min at ambient temperature.

Techniques: Sequencing, Isolation

Journal: Clinical Chemistry

Article Title: Measurement Biases Distort Cell-Free DNA Fragmentation Profiles and Define the Sensitivity of Metagenomic Cell-Free DNA Sequencing Assays

doi: 10.1093/clinchem/hvab142

Figure Lengend Snippet: cfDNA isolation and library preparation kits compared in this study.

Article Snippet: For the tuberculosis patient samples, 10 mL of urine was mixed with 2 mL Streck cell-free DNA urine preserve (Streck, USA) and centrifuged at 3000 g for 30 min at ambient temperature.

Techniques: Isolation, DNA Purification, DNA Extraction, Modification