Journal: Nature Communications

Article Title: Standardized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA

doi: 10.1038/s41467-021-25576-6

Figure Lengend Snippet: Stool samples collected from omnivorous donors and processed into a single standardized matrix by NIST was spiked with ATCC CoV-2 RNA or BCoV vaccine. Spiked stool was preserved in the OMNIgene-GUT Kit (OG), Zymo DNA/RNA shield buffer (ZY), and PBS (as indicated in the tab on the top). RNA was extracted from these samples by two independent users, each in duplicate, using the MagMAX Viral/Pathogen Kit (MM; green), QIAamp Viral RNA Mini Kit (QA; orange), or Zymo Quick-RNA Viral Kit (ZY; purple) as indicated on the x -axis. RNA was assayed using ddPCR. a Absolute concentration of SARS-CoV-2 RNA assayed by ddPCR targeting the N1 gene is plotted on the y -axis. NIST stool matrix was spiked with 10 3 (triangle) or 10 4 (square) copies of ATCC synthetic SARS-CoV-2 RNA. b Absolute concentration of BCoV RNA assayed by ddPCR targeting the M gene is plotted on the y -axis. NIST stool matrix was spiked with 1:10 diluted (triangle) or undiluted (square) BCoV vaccine. Control samples with no spiked in RNA (none; circle) were included in duplicate to estimate LoB. U stands for undetermined and marks samples with no detectable RNA above LoB. Two-sided paired T tests were performed on n = 4 independent extractions for each spike-in condition. Associated statistics are summarized in Supplementary Data . Source data are provided as a Source data file.

Article Snippet: NIST stool matrix was spiked with 10 3 (triangle) or 10 4 (square) copies of ATCC synthetic SARS-CoV-2 RNA. b Absolute concentration of BCoV RNA assayed by ddPCR targeting the M gene is plotted on the y -axis.

Techniques: Concentration Assay, Control

Journal: Cancer cell

Article Title: Comprehensive Molecular Characterization Identifies Distinct Genomic and Immune Hallmarks of Renal Medullary Carcinoma

doi: 10.1016/j.ccell.2020.04.002

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Control DNA was used from Promega (Human Genomic DNA Female N 30742202/Male N 30993901).

Techniques: Control, Virus, Recombinant, Library Quantification, DNA Methylation Assay, Empire Assay, Imaging, Sequencing, Plasmid Preparation, Software

Journal:

Article Title: Enhancement of DNA repair in human skin cells by thymidine dinucleotides: Evidence for a p53-mediated mammalian SOS response

doi:

Figure Lengend Snippet: The effect of pTpT on the repair rate of thymine dimers and (6–4) photoproducts. Preconfluent cultures of newborn fibroblasts were supplemented with either 100 μM pTpT or an equal volume of diluent for 5 days before exposure to 50 mJ/cm2 UVB. The cells then were collected at various time points, and the genomic DNA was isolated. Thymine dimer (A) and (6–4) photoproduct (B) content were determined as described in Materials and Methods. Samples harvested immediately after irradiation (time 0) were set at 100%, and all time points were calculated as a percent of these values. No consistent effect of pTpT on the degree of initial DNA damage (time 0 values) was seen. Each normalized time point is the average of duplicate blots. Data for a representative donor (one of three separate experiments) are shown. The difference between diluent- and pTpT-treated cells was statistically significant [P < 0.013 for thymine dimers and P < 0.028 for (6–4) photoproducts; one-tailed t test].

Article Snippet: To evaluate the uniformity of DNA sample loading, each slot blot also was hybridized with 32 P-labeled human genomic DNA (Promega) ( 22 ).

Techniques: Isolation, Irradiation, One-tailed Test