DOI: 10.5061/dryad.37pvmcvzx
title: Data from: Bulk-seq results from peripheral blood mononuclear cells (PBMCs) of VKH patients and proteomic profiling of shAPOE-transduced HMC3 cells were employed to uncover potential downstream targets of APOE

description: Autoimmune uveitis (AU) is a category of sight-threatening diseases with
 different pathological causes. Transcriptomic analysis of AU patients
 revealed a highly oxidative stress profile as well as an upregulated
 apolipoprotein E (APOE) expression in their peripheral blood mononuclear
 cells (PBMC). To further investigate the role of APOE in the disease, we
 performed proteomic analysis on HMC3 transfected with lentivirus-mediated
 APOE knockdown to explore potential downstream targets of APOE. Clinical
 data were integrated to enhance the overall credibility and accuracy of
 the findings.
description: # Data from: Bulk-seq results from peripheral blood mononuclear cells
 (PBMCs) of VKH patients and proteomic profiling of shAPOE-transduced HMC3
 cells were employed to uncover potential downstream targets of APOE
 Dataset DOI:
 [10.5061/dryad.37pvmcvzx](https://doi.org/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.