Tissue sections were loaded into the GeoMx platform and scanned for an immunofluorescent signal. A geometric strategy was employed for selection of regions of interest (ROIs) which were segmented on the basis of HBsAg staining and presence of immune cell infiltrate
Hybridization protocol
n.a.
Scan protocol
n.a.
Description
HBV_HIV_coninfectio
Data processing
Quality control checks and data analysis were performed in the GeoMx DSP Data Analysis suite. All regions of interest (ROI) had acceptable sequencing quality metrics after examination of the raw, trimmed, stitched, aligned and deduplicated reads, and the sequencing saturation (>60%). An expression value per gene target per ROI was generated in GeoMx DSP Analysis Suite through the compilation of multiple probes, within the NanoString GeoMx Human Whole Transcriptome Atlas probe mix, for each transcript. The manufacturer’s recommended threshold for the detection of genes in referred to as the Limit of Quantification (LOQ); the LOQ is 2 geometric standard deviations above the geometric mean. The AOI from PT2, PT1 and PT3 tissues were filtered to include only the genes detected over the LOQ in 3 or more AOI: 9672 genes. The data were then quantile normalised and the performance of the normalisation was assessed by the standardisation of housekeeping genes and distribution of total gene expression between ROI
