Dataset DOI: 10.5061/dryad.37pvmcvzx

Description of the data and file structure

Description of the data and file structure

The following content comprises the raw data and analytical results from bulk-seq sequencing of VKH patient blood and proteomic mass spectrometry of HMC3 cells used in this study. Specifically:

1. "Proteomics.zip" contains the raw mass spectrometry files from the HMC3 proteomic analysis.

2. "Differentially_expressed_proteins.csv"provides the analysis results of differentially expressed proteins from the HMC3 proteomics study.

3. "VKH_bulk-seq.zip" includes the raw bulk-seq data of PBMCs from VKH patients and age-matched healthy controls.

4. "Differentially_expressed_genes_ratio.csv"contains the analytical results of the bulk-seq data of PBMCs from VKH patients and age-matched healthy controls.

For detailed descriptions of the fields in the "CSV" results files, please refer to the below content.

Files and variables

File: Proteomics.zip

Description: Proteomic raw data (including RAW files, etc.) from HMC3 cells transducted with APOE-knockdown lentivirus.

File: Differentially_expressed_proteins.csv

Description: Proteomic analysis was performed on microglia transducted with lentivirus to knock down APOE expression, with results compiled into a CSV file. Specific proteins were identified and quantified based on peptide information, and expression ratios relative to baseline were calculated for intuitive data visualization.

Variables

• Protein accession: Characteristic numbering of different proteins.
• Protein description: Detailed description of protein name.
• Gene name: Gene name.
• Coverage [%]: Amino acid coverage in protein sequence.
• Peptides: The total number of identified different peptide segments.
• Unique peptides: The number of specific peptide segments contained.
• Intensity CN:
  • Intensity: Identified protein abundance.
  • CN: HMC3 cell transduced with empty lentiviral vector (serving as a control).
• Intensity S100:
  • Intensity: Identified protein abundance.
  • S100: HMC3 cells stimulated with IL-17a and IFN-γ.
• Intensity shRNA:
  • Intensity: Identified protein abundance.
  • shRNA: HMC3 cells transduced with lentiviral vector expressing APOE short-hairpin RNA to knock down APOE.
• CN: HMC3 cells transduced with empty lentiviral vector (serving as a control). Values below indicate the relative expression level of a specific protein within this group.
• S100: HMC3 cells stimulated with IL-17a and IFN-γ. Values below indicate the relative expression level of a specific protein within this group.
• shRNA: HMC3 cells transduced with lentiviral vector expressing APOE short-hairpin RNA to knock down APOE. Values below indicate the relative expression level of a specific protein within this group.

File: Differentially_expressed_genes_ratio.csv

Description: Analytical analysis was performed on sequencing data from peripheral blood mononuclear cells (PBMCs) of VKH patients. Results were scaled to log2 values and converted to a CSV file displaying fold change (VKH vs. control) for intuitive data interpretation.

Variables

• genes_ID: Gene name.
• baseMean: The average expression level of each gene in all samples.
• log2FoldChange: log2-scale fold change in gene expression.
• lfcSE: Estimation of the standard error for log2 fold change.
• stat: statistic.
• pvalue: Indicators for evaluating significant differences.
• padj: Adjusted p-value.

File: VKH_Bulk-seq.zip

Description: bulk-seq raw data of PBMCs from VKH patients and age-matched healthy controls.

Human subjects data

All data collected from human subjects have been de-identified to protect participant privacy. Direct identifiers, such as names and medical record numbers, have been removed. Written informed consent was obtained from all participants, which explicitly authorized the publication of de-identified data in the public domain.