Confirm with Sowmya

[shkwon17]

• [x] "...However, we manually excluded Aβ-positive spots that were falsely annotated due to glare artifacts in the Aβ channel (Figure S9B). This preprocessing step for spot-level QC filtered out XX spots, yielding a total of XXXX spots across the 7 samples from 3 AD donors for downstream analyses..."

• Here, we need the number of spots that were filtered due to glare artifacts and the total number of spots counted for downstream analyses. All those XXs.

• [ ] Figure captions for Figure S16 about the p-value thresholds and odd ratios.

• Especially, the odd ratio in the gene set enrichment analysis with the mostafavi dataset, we need to create a 2x2 matrix to look into the odd ratio of zero - namely, to check if it is really 0 or a very small decimal close to 0 like 0.00000000X.

• image demonstration

[shkwon17]

what changes were made and how they led to the differences in results before and after the re-run, especially when comparing the Mostafavi dataset to our depleted Ab-relevant gene set.

01_mostafavi_enriched.pdf 01_mostafavi_depleted.pdf

[shkwon17]

Update on 03-31-2023 after coding session:

• [x] Sowmya can update the plots for Mostafavi to adjust the color gradient, essentially making what is currently dark red more yellowish for consistency.

• One option is to add artificial boxes (with a p-value of 1.2ish), which Sang Ho can remove in Illustrator.

• The Grumman plots are the same before and after, so Sang Ho will keep the previous ones as they are in the manuscript.

• Sang Ho will revise the figure captions and ask Sowmya and Leo for proofreading.

[shkwon17]

https://jhu-genomics.slack.com/archives/C01GJ0F731Q/p1680463344341639

[shkwon17]

• [x] Sang Ho will revise the figure with the updated plots.

[shkwon17]

Newly updated plots:

04_grubman_depleted-3.pdf 04_grubman_enriched-4.pdf 01_mostafavi_enriched-2.pdf 01_mostafavi_depleted-2.pdf

[shkwon17]

[shkwon17]

• [ ] Just to make sure which one is right, in terms of the boxes: 1) depleted Ab vs Ex neurons and 2) depleted Ab and Oligos

04_grubman_depleted-2.pdf 04_grubman_depleted-3.pdf

[shkwon17]

• [ ] Confirm with Leo and Sowmya the figure captions about the GSEA results AFTER Sang Ho revises the figure S13

Figure S13. Enrichment of neurodegeneration- and dementia-related gene sets in Aβ-associated microenvironments. (A) MAGMA associations of GWAS datasets for Alzheimer’s disease (AD, Jansen et al. 2019), frontotemporal dementia (FTD, Ferrari et al. 2014), and Parkinson’s disease (PD, Nalls et al. 2019) with Aβ-associated microenvironments profiled in human ITC. The results were presented in a heatmap, with the color scale indicating −log10 (p-value) and the numbers in the boxes indicating odd ratios for the enrichment. The p-value was thresholded at p = XXXX, allowing for the visualization of the most significant associations. (B) Spatial gene set enrichment analysis with a bulk RNA-seq dataset of dorsolateral prefrontal cortex (DLPFC) collected from the ROSMAP cohort (Mstafavi et al. 2018). M109_Total refers to a gene module of 390 coexpressed genes strongly associated with cognitive decline and Aβ pathology in AD. M109_Top 112 is a subset of M109 containing top 112 interesting genes selected by an initial Baysian network, while M109_Valid 21 is a gene set containing 21 validated genes. These gene sets were compared and tested for their associations with Aβ-associated microenvironments profiled for enriched (top) and depleted (bottom) gene sets in the human ITC. The results were presented in a heatmap, with the color scale indicating −log10 (p-value) and the numbers in the boxes indicating odd ratios for the enrichment. The p-value was thresholded at p = XXXX, allowing for the visualization of the most significant associations. (C) Spatial gene set enrichment analysis with a scRNA-seq dataset for AD (Grubman et al. 2019). Grubman et. al. identified AD-associated DEGs between case and control across 6 different cell types in the human entorhinal cortex, which were found to overlap with those identified in human DLPFC (Mathys et al. 2019). These cell type-specific gene sets were compared and tested for their associations with the Aβ-associated microenvironment in the human ITC, separated by enriched (top) and depleted (bottom) gene sets. The results are presented in a heatmap, with the color scale indicating −log10 (p-value) and the numbers in the boxes indicating odd ratios for the enrichment. The p-value was thresholded at p = XXXX, allowing for the visualization of the most significant associations.