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.本仓库配套于以下论文：《同位素编码空间生物学技术鉴定淀粉样斑块年龄依赖性结构成熟与突触丢失》。 转录组数据以.csv格式文件存储。针对App NL-F/NL-F小鼠模型，18月龄数据存储于norm_Quant_18_GeoMX.csv文件，10月龄数据存储于norm_Quant_10_GeoMX.csv文件。 下一代测序（Next Generation Sequencing, NGS）与生物探针的质量控制（Quality Control, QC）分析采用GeoMX DSP默认参数（GeoMX NGS Pipeline版本2.3.4）完成。所有后续分析均在R语言环境中进行[R开发团队，奥地利维也纳；https://www.R-project.org/]。 若探针计数过低，或未通过遵循NanoString指南的Grubbs异常值检验，则将其从分析中剔除。在10月龄组中，因斑点形态模糊、存在多个斑块或MALDI检测信号强度极低，共排除9个感兴趣区域（regions of interest, ROIs）。同理，18月龄组因相同原因排除6个感兴趣区域。完成数据过滤后，对感兴趣区域（areas of interest, AOIs）内的每个靶标计算几何均值。 将本次质量控制结果与标准NanoString流程所得结果进行比对，结果显示异常值检测整体一致性良好，观测到的微小差异大概率源于所使用检测参数的细微差别。最终使用`preprocessCore` R包提供的`normalize:quantiles`函数完成分位数归一化。 名为spectra_10mo_csv.zip与spectra_18mo_csv.zip的压缩文件包含正线性模式下的基质辅助激光解吸电离质谱成像（Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging, MALDI MSI）数据。正线性模式氮指数（LP）流程如下：提取靶标质荷比（m/z）区域（例如淀粉样蛋白Aβ₁₋₄₂），完成归一化、平滑处理、ALS基线校正、半高全宽（Full Width at Half Maximum, FWHM）峰分析，并导出注释结果。更多细节与代码可于GitHub获取：https://github.com/MaciejDulewiczGU/MaldiGeoMxSpatialTranscriptomicsIsotopeaker。在https://maciejdulewiczgu.shinyapps.io/MALDI_GEOMX_VOLCANO/的“SPECTRA VIEWER”标签页中，可查看并下载10月龄与18月龄组的所有MALDI质谱数据。 名为RP_Mode_MALDI_MSI.zip的压缩文件包含用于计算反射模式氮指数的基质辅助激光解吸电离质谱成像数据。更多细节与数据分析方法可于GitHub获取：https://github.com/MaciejDulewiczGU/MaldiGeoMxSpatialTranscriptomicsIsotopeaker。