Isotope Encoded Spatial Biology Identifies Amyloid Plaque-Age-Dependent Structural Maturation and Synaptic Loss - All datasets

This repository contains supplementary data for the article: Isotope Encoded Spatial Biology Identifies Amyloid Plaque-Age-Dependent Structural Maturation and Synaptic Loss.

Transcriptomic data were deposited in .csv files. For the App NL-F/NL-F mouse model, the 18-month data are in the norm_Quant_18_GeoMX.csv file and the 10-month data are in the norm_Quant_10_GeoMX.csv file. The quality control (QC) analysis for Next Generation Sequencing (NGS) and Biological Probe QC was conducted using the default GeoMX DSP parameters (GeoMX NGS Pipeline version 2.3.4). All subsequent analyses were performed in R [R Core Team, Vienna, Austria; https://www.R-project.org/]. Probes were excluded from the analysis if their counts were too low or if they failed the Grubbs outlier test according to NanoString guidelines. In the 10-month-old group, nine regions of interest (ROIs) were excluded due to ambiguous spot morphology, the presence of more than one plaque, or very low intensity in the MALDI results. Similarly, six ROIs from the 18-month-old group were excluded for the same reason. After filtering the data, the geometric mean was calculated for each target within the areas of interest (AOIs). The QC results were then compared with those obtained from the standard NanoString pipeline, revealing generally consistent outcomes in terms of outlier detection. Any minor discrepancies observed are likely attributable to slight differences in the test parameters used. Finally, quantile normalization was applied using the `normalize:quantiles` function provided by the `preprocessCore` R package.

The zip files titled spectra_10mo_csv.zip and spectra_18mo_csv.zip contain MALDI MSI data with a linear positive mode. Nitrogen index LP (linear positive mode): Extracts the target m/z region (e.g. amyloid Aβ₁₋₄₂), performs normalisation, smoothing, ALS baseline correction, FWHM peak analysis and exports annotated results. More details and code are available on github: https://github.com/MaciejDulewiczGU/MaldiGeoMxSpatialTranscriptomicsIsotopeaker. Under the ‘SPECTRA VIEWER’ tab, all MALDI spectra from 18-month and 10-month groups can be viewed and downloaded on https://maciejdulewiczgu.shinyapps.io/MALDI_GEOMX_VOLCANO/

The zip file titled RP_Mode_MALDI_MSI.zip contains the reflector mode data that was used to calculate the RP Nitrogen Index. More details and how to analyse the data can be found on github: https://github.com/MaciejDulewiczGU/MaldiGeoMxSpatialTranscriptomicsIsotopeaker.