Extended Data Fig. 8: NanoString GeoMx experiment design and analysis.
From: COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
a, Overview of spatial profiling experiments. b, Distribution of sequencing saturation (y axis, %) for WTA and CTA AOIs (x axis). c, d, SARS-CoV-2 signature score (y axis) for each WTA (c) and CTA (d) AOI (dots) from each donor (x axis). e, Overlap of WTA and CTA genes. f, g, Agreement between WTA and CTA. f, Distribution (box, interquartile range; white point, median; violin range, min–max) of Pearson correlation coefficients (y axis) between WTA and CTA profiles (for common genes across 296 AOIs). g, Pearson correlation coefficient (y axis) of WTA and CTA common genes for each AOI pair (dot) from each donor (x axis), sorted by distance between WTA and CTA sections (blue, 10 mm; orange, 20 mm; green, 40 mm). h, Cell composition differences between PanCK+ and PanCK− alveolar AOIs and between AOIs from COVID-19 (n = 9, 161 AOIs) and healthy (D22–24, 40 AOIs) lungs. Expression scores (colour bar) of cell type signatures (rows) in PanCK+ (left) and PanCK− (right) alveolar AOIs (columns) in CTA data from different donors (top colour bar). i–k, Differential gene expression in COVID-19 versus healthy lung. Left: significance (−log10(P), y axis) and magnitude (log2(fold change), x axis) of differential expression of each gene (dots) in WTA for PanCK− (i, 112 COVID-19 versus 20 healthy), and in CTA for PanCK+ (j, 69 COVID-19 versus 18 healthy) and PanCK− (k, 92 COVID-19 versus 22 healthy) alveoli. Horizontal dashed line, FDR = 0.05; vertical dashed lines, |log2(fold change)| = 2. Right: significance (−log10(q)) of enrichment (permutation test) of different pathways (rows). l, m, Changes in gene expression in SARS-CoV-2 high versus low AOIs within COVID-19 lungs in WTA data. l, PanCK− alveolar AOIs (dots) rank ordered by their SARS-CoV-2 signature score (y axis) in WTA data, and partitioned to high (red), medium (grey) and low (blue) SARS-CoV-2 AOIs. m. Significance (−log10(P), y axis) and magnitude (log2(fold change), x axis) of differential expression of each gene (dots) in WTA data between SARS-CoV-2 high and low AOIs for PanCK− alveoli (ROIs: 11 high, six medium, 95 low). Horizontal dashed line, FDR = 0.05.
