Quantified processed microarray data for 22 individuals with and without proliferative retinopathy

Quality control from RNA extraction was performed using the Agilent bio-analyzer, processed using the Illumina™ TotalPrep™-96 RNA Amplification Kit (ThermoFisher 4393543), hybridized to Illumina HT12v4 microarrays (Catalog number: 4393543), and scanned on an Illumina HiScan scanner [22] [23]. For each of the 22 individuals, three biological replicates were profiled, with each sample being assessed at both standard glucose conditions (11mM of glucose), as well as high glucose conditions (30mM of glucose). Biological replicates were split from the same mother flask; cells were grown in separate flasks and run on different microarray plates on different days. Each biological replicate was generated from a separate frozen aliquot of that cell line. The gene expression data comprised a total of 144 samples from 22 individuals (3 replicates per individual and treatment, except for 3 individuals with 5 replicates). Gene expression was assessed in two conditions, standard glucose and high glucose, and generated from four different groups of gene expression arrays run at a given time that were carefully designed to minimize potential batch effects. BeadChip data were extracted using GenomeStudio (version GSGX 1.9.0) and the raw expression and control probe data from the four different batches were preprocessed using a lumiExpresso function in the lumi R package [8, 9] in three steps: (i) background correction (lumiB function with the bgAdjust method); (ii) variance stabilizing transformation (lumiT function with the log2 option); (iii) normalization (lumiN function with the robust spline normalization (rsn) algorithm that is a mixture of quantile and loess normalization). To remove unexpressed probes, we applied a detection filter to retain probes with strong true signal by applying Illumina BeadArrays detection p-values < 0.01 followed by removing probes that did not have annotated genes, resulting in a total of 15,591 probes.RNA提取的质量控制采用安捷伦生物分析仪（Agilent bio-analyzer）完成，样本处理使用Illumina™ TotalPrep™-96 RNA扩增试剂盒（ThermoFisher 4393543），随后与Illumina HT12v4基因芯片（目录号：4393543）进行杂交，并在Illumina HiScan扫描仪（Illumina HiScan scanner）上完成扫描[22, 23]。 针对22名受试者中的每一位，均设置3次生物学重复进行检测，且每份样本均在标准葡萄糖浓度（11mM）与高葡萄糖浓度（30mM）两种培养条件下完成评估。生物学重复样本均来自同一母培养瓶：细胞分别接种于不同培养瓶中培养，于不同日期在不同基因芯片板上开展实验，每份生物学重复样本均来自该细胞系的独立冻存分装样本。 本基因表达数据集共包含22名受试者的144份样本（每名受试者每种处理条件设3次重复，其中3名受试者除外，其重复次数为5次）。 基因表达检测涵盖标准葡萄糖与高葡萄糖两种培养条件，实验分为4个批次的基因芯片检测完成，该批次设置经精心设计以最大程度降低潜在的批次效应。 基因芯片（BeadChip）原始数据通过GenomeStudio软件（版本GSGX 1.9.0）提取；随后，针对4个批次的原始表达量与对照探针数据，采用R语言lumi包（lumi R package）中的lumiExpresso函数完成三步预处理：（1）背景校正：使用bgAdjust方法的lumiB函数；（2）方差稳定变换：使用log2选项的lumiT函数；（3）标准化：采用稳健样条标准化（rsn）算法的lumiN函数，该算法结合了分位数标准化与局部加权回归（loess）标准化。 为剔除未表达的探针，我们设置检测过滤规则以保留具有显著真实信号的探针：首先保留Illumina基因芯片检测P值<0.01的探针，随后移除无对应注释基因的探针，最终共保留15591个探针。