Journal: bioRxiv

Article Title: Intrinsic OASL expression licenses interferon induction during influenza A virus infection

doi: 10.1101/2025.03.14.643375

Figure Lengend Snippet: A ) UMAP visualization of scRNA-seq data from HBECs, with cells labeled based on cell types. B ) Proportion of cells expressing OASL, IFIT3, DDX60, ISG15, or IRF1 and C) expression counts divided by donor. D) The cell type composition of positive cells for each candidate gene separated and colored by cell types. E) Fraction of cells within each cell type expressing the candidate ISGs.

Article Snippet: Reactions were incubated at 45°C for 50 min and 95°C for 2 min and held at 4°C; cDNA was stored at -20 and subsequently used for quantitative PCR. qPCR reactions were setup by combining 10 μL of TaqMan fast advanced master mix (Applied Biosystems), 1 μL of probe ( OASL; Applied Biosystems: Hs00984387_m1, IFIT3 ; Applied Biosystems: Hs01922752_s1, DDX60 ; Applied Biosystems: Hs01102712_m1, ISG15 ; Applied Biosystems: Hs01921425_s1, IRF1 ; Applied Biosystems: Hs00971965_m1), 1 μL of cDNA and 8 μL of nuclease-free water.

Techniques: Labeling, Expressing

Journal: bioRxiv

Article Title: SomaScan Bioinformatics: Normalization, Quality Control, and Assessment of Pre-Analytical Variation

doi: 10.1101/2024.02.09.579724

Figure Lengend Snippet: Venn diagram showing the SOMAmer overlap (based on “SeqId” identifiers) between the 1.3K, 5K, 7K, and 11K SomaScan assays.

Article Snippet: For each human protein SOMAmer in the plasma 7K assay, we calculated the Spearman’s correlation between the fully normalized RFU values from the adat file provided by SomaLogic using external references (a file designated with the “hybNorm.medNormInt.plateScale.calibrate.anmlQC.qcCheck.anmlSMP” suffix) and the full normalization described here using internal references (“hyb.msnCal.ps.cal.msnAll”).

Techniques:

Journal: bioRxiv

Article Title: SomaScan Bioinformatics: Normalization, Quality Control, and Assessment of Pre-Analytical Variation

doi: 10.1101/2024.02.09.579724

Figure Lengend Snippet: Distribution of Spearman’s correlation estimates for the 7,289 human protein SOMAmers in the 7K plasma SomaScan assay, calculated over nearly 1,800 human donor samples from the BLSA . For each SOMAmer, the correlation was calculated between the fully normalized RFU values from SomaLogic’s pipeline using external references and the full normalization described here using internal references.

Article Snippet: For each human protein SOMAmer in the plasma 7K assay, we calculated the Spearman’s correlation between the fully normalized RFU values from the adat file provided by SomaLogic using external references (a file designated with the “hybNorm.medNormInt.plateScale.calibrate.anmlQC.qcCheck.anmlSMP” suffix) and the full normalization described here using internal references (“hyb.msnCal.ps.cal.msnAll”).

Techniques: Clinical Proteomics