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: bioRxiv

Article Title: Unmasking Human T Cell Receptor Germline Diversity: 335 Novel Alleles Identified in 47 Pangenome Reference Individuals Using the gAIRR Suite

doi: 10.1101/2025.05.24.655452

Figure Lengend Snippet: (A) Discovery of novel TR alleles. High-quality genome assemblies from the HPRC were analyzed using gAIRR-annotate to identify both reference TR alleles from the IMGT database (blue) and candidate novel alleles (red). (B) Crosscheck between gAIRR-annotate and gAIRR-call results, and creation of a flanking sequence database. This panel illustrates the orthogonal validation process between two independent pipelines. On one side, gAIRR-annotate identifies TR alleles from genome assemblies. On the other, gAIRR-seq captures genomic DNA for targeted sequencing, and gAIRR-call infers alleles from NGS reads. The allele database used by both pipelines includes IMGT reference alleles (blue) and candidate novel alleles (red) discovered in panel (a). Annotated alleles and called alleles are crosschecked to identify validated novel alleles (brown), which are then included in the final allele database. Flanking sequences are extracted to construct a comprehensive flanking sequence database.

Article Snippet: Genomic DNA reference materials for these subjects were obtained from the Coriell Institute ( https://www.coriell.org ).

Techniques: Sequencing, Biomarker Discovery, Construct