Bayesian hidden mark interaction model for detecting spatially variable genes in imaging-based spatially resolved transcriptomics data.

Recent technology breakthroughs in spatially resolved transcriptomics (SRT) have enabled the comprehensive molecular characterization of cells whilst preserving their spatial and gene expression contexts. One of the fundamental questions in analyzing SRT data is the identification of spatially variable genes whose expressions display spatially correlated patterns. Existing approaches are built upon either the Gaussian process-based model, which relies on kernels, or the energy-based Ising model, which requires gene expression to be measured on a lattice grid.

Assay of DNA-binding proteins with a dsDNA-coupled plate.

Objectives: This paper fabricated a cost-effective dsDNA-coupled plate (dcPlate) and applied it to measure the abundance and DNA-binding activity of a DNA-binding protein (DBP).

Design And Methods: The dcPlate was manufactured by covalently immobilizing an amino-modified oligonucleotide in wells of the plate coated with N-oxysuccinimide esters. The dcPlate was applied to measure the abundance of DNA-binding activity of a DBP in the same four steps, including protein incubation, primary antibody binding, enzyme-linked secondary antibody binding, and colorimetric development.

A method for fabricating uni-dsDNA microarray chip for analyzing DNA-binding proteins.

This paper describes an approach for preparing unimolecular double-stranded DNA (uni-dsDNA) microarray chip. In this method, the various target oligonucleotides containing a reverse complementary sequence at 5' end were firstly annealed to a same universal oligonucleotide with amino group at 5' end and immobilized on aldehyde-derivatized glass slide. An on-chip DNA polymerization reaction was then performed to elongate the universal oligonucleotides.

Evaluating the binding affinities of NF-kappaB p50 homodimer to the wild-type and single-nucleotide mutant Ig-kappaB sites by the unimolecular dsDNA microarray.

This study investigated the binding affinities of NF-kappaB p50 homodimer to the wild-type and single-nucleotide mutant Ig-kappaB sites by the unimolecular dsDNA microarray which was fabricated with a novel scheme. The importance of each nucleotide of Ig-kappaB site for the sequence-specific p50p50/Ig-kappaB interaction was thus evaluated. The results demonstrate that the nucleotides at different positions contribute differently to the p50p50/Ig-kappaB binding interaction.