PubMed · 11579778
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K Geissler. Foreign affairs.. https://pubmed.ncbi.nlm.nih.gov/11579778/
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MOTIVATION: 10x Genomics VisiumHD enables spatial transcriptomics at 2 µm × 2 µm resolution but exhibits slide-specific, non-periodic striping artifacts due to lane-width variability. These multiplicative row/column effects distort bin total counts and can bias downstream analyses. The state-of-the-art destriping approach is the normalization procedure used as a preprocessing step in bin2cell; it applies sequential high-quantile row- then column-wise normalization, which is asymmetric and can introduce edge effects/macro-stripes and distortions of large-scale total-count structure. RESULTS: We propose a statistical destriping approach that leverages nuclei segmentation from the co-registered H&E image. Assuming transcript abundance is constant within each nucleus, we model bin counts with a negative binomial distribution whose mean is a product of a nucleus-specific concentration and row- and column-specific stripe-factors reflecting lane-width variation. We fit all parameters in a generalized linear modeling framework with cross-validated regularization on stripe-factors and iterative dispersion estimation, and use the fitted parameters to correct the observed counts into a destriped image. On synthetic data with known ground truth, our method improves stripe-factor estimation accuracy and reduces error in corrected counts relative to bin2cell and bin2cell-derived baselines. Across four public VisiumHD slides, it consistently lowers striping intensity while substantially better preserving biological signal present in the large-scale global count structure and avoiding the artifacts introduced by other methods. AVAILABILITY AND IMPLEMENTATION: All source code and links to publicly available data used for this study are available at https://github.com/paolamalsot/destriping-GLM.
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Native TALL-1 (B-cell activation factor, BAFF; also known as BlyS) was initially described as a homotrimer, but Liu and colleagues claim that it is a 60-subunit complex on the basis of their results from X-ray crystallography and size-exclusion chromatography. They consider TALL-1 60-mers to be the biologically active form, and the arrangement of the 60-mers resembles that of the capsid of satellite tobacco necrosis virus. Here we show that active TALL-1 is trimeric under normal physiological conditions and that formation of higher-order oligomers is an artefact of tagging the amino terminus of the protein with a histidine tag.