List of differentially expressed genes for "Basigin is necessary for normal decidualization of human uterine stromal cells"

List of differentially expressed genes in human endometrial stromal cells with knockdown of Basigin (BSG) gene expression during decidualization. The BSG siRNA or negative scrambled control siRNA were transfected into human endometrial stromal cells (HESCs) following the protocol of siLentFect™ Lipid (Bio-Rad, Hercules, CA. Following complete knock down of BSG in HESCs (72 hours after adding siRNA), HESCs were treated with medium containing estrogen, progesterone and cAMP to induce decidualization. BSG siRNA and negative control scrambled siRNA were added to the cells every four days (day 0, 4) over the course of the decidualization protocol. Total RNA was harvested at day 6 of the decidualization protocol for microarray analysis. Microarray analysis was performed at the University of Illinois at Urbana-Champaign Roy J. Carver Biotechnology Center. Briefly, 0.2 micrograms of total RNA were labeled using the Agilent two color QuickAmp labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer’s protocol. The optional spike-in controls were not used. Samples were hybridized to Human Gene Expression 4x44K v2 Microarray (Agilent Technologies, Santa Clara, CA) in an Agilent Hybridization Cassette according to standard protocols. The arrays were then scanned on an Axon GenePix 4000B scanner and the images were quantified using Axon GenePix 6.1. Microarray data pre-processing and statistical analyses were done in R (v3.6.2) using the limma package (3.42.0 (Ritchie et al., 2015). Median foreground and median background values from the 4 arrays were read into R and any spots that had been manually flagged (-100 values) were given a weight of zero. The background values were ignored because investigations showed that trying to use them to adjust for background fluorescence added more noise to the data; background was low and even for all arrays, therefore no background correction was done. The individual Cy5 and Cy3 fluorescence for each array were normalized together using the quantile method 3 (Yang and Thorne, 2003). Agilent's Human Gene Expression 4x44K v2 Microarray has a total of 45,220 probes: 1224 probes for positive controls, 153 negative control, 823 labeled “ignore” and 43,118 labeled “cDNA”. The pos+neg+ignore probes were used to ascertain the background level of fluorescence (6, on the log2 scale) then discarded. The cDNA probes comprise 34,127 unique 60mer probes, of which 999 probes are spotted 10 times each and the rest one time each. We averaged the replicate probes for those spotted 10 times and then fit a mixed model that had treatment and dye as fixed effects and array pairing as a random effect (Phipson et al., 2016; Smyth et al., 2005). After fitting the model but before False Discovery Rate (FDR) correction (Benjamini and Hochberg, 1995), probes were filtered out by the following criteria: 1) did not have at least 4/8 samples with expression values > 6 (14,105 probes removed), 2) no longer had an assigned Entrez Gene ID in Bioconductor’s HsAgilentDesign026652.db annotation package (v3.2.3; 2,152 probes removed) (Huber et al., 2015), 3) mapped to the same Entrez Gene ID as another probe but had a larger p-value for treatment effect (4,141 probes removed). This left 13,729 probes representing 13,729 unique genes. <b>*Please note: that there is a discrepancy between the file and the readme as this plain text is the actual data file of this dataset.</b>

本数据集收录了在人类子宫内膜基质细胞中，经Basigin（BSG）基因表达敲低处理期间差异表达的基因列表。在子宫内膜基质细胞（HESCs）中，通过siLentFect™脂质体转染技术（Bio-Rad，Hercules，CA）引入BSG小干扰RNA（siRNA）或阴性对照 scrambled siRNA。遵循该方案，在siRNA添加后72小时，实现BSG在HESCs中的完全敲低后，用含有雌激素、孕酮和cAMP的培养基处理HESCs以诱导蜕膜化。在蜕膜化过程中，每四天（第0天、第4天）向细胞中加入BSG siRNA和阴性对照 scrambled siRNA。在第6天蜕膜化方案结束时，收获总RNA进行微阵列分析。微阵列分析由伊利诺伊大学厄巴纳-香槟分校Roy J. Carver生物技术中心执行。简而言之，使用Agilent双色QuickAmp标记试剂盒（Agilent Technologies，Santa Clara，CA）根据制造商的协议对0.2微克的总RNA进行标记。未使用可选的spike-in对照。将样本与Human Gene Expression 4x44K v2微阵列（Agilent Technologies，Santa Clara，CA）在Agilent杂交盒中进行杂交，遵循标准方案。随后，使用Axon GenePix 4000B扫描仪扫描阵列，并使用Axon GenePix 6.1对图像进行量化。在R（v3.6.2）中使用limma包（3.42.0，Ritchie等，2015）进行微阵列数据的预处理和统计分析。将4个阵列的中值前景和中值背景值读入R中，并赋予任何手动标记的斑点（-100值）零权重。由于调查表明，尝试使用背景值调整背景荧光会增加数据噪声；所有阵列的背景均较低且均匀，因此未进行背景校正。使用分位数方法3（Yang和Thorne，2003）对每个阵列的Cy5和Cy3荧光进行联合归一化。Agilent的Human Gene Expression 4x44K v2微阵列包含总计45,220个探针：1,224个探针用于阳性对照，153个探针用于阴性对照，823个探针标记为“忽略”，43,118个探针标记为“cDNA”。使用pos+neg+ignore探针确定荧光背景水平（6，以log2刻度计），然后丢弃。cDNA探针包括34,127个独特的60mer探针，其中999个探针重复10次，其余的只重复1次。对于重复的探针，我们取其平均值，然后拟合一个混合模型，该模型以处理和染料作为固定效应，阵列配对作为随机效应（Phipson等，2016；Smyth等，2005）。在拟合模型但进行假发现率（FDR）校正（Benjamini和Hochberg，1995）之前，根据以下标准筛选探针：1）至少4/8个样本的表达值大于6（移除14,105个探针），2）在Bioconductor的HsAgilentDesign026652.db注释包（v3.2.3；移除2,152个探针）中没有分配Entrez Gene ID（Huber等，2015），3）映射到与另一个探针相同的Entrez Gene ID，但治疗效应的p值更大（移除4,141个探针）。这留下了13,729个探针，代表13,729个独特的基因。<b>请注意：文件与readme之间存在差异，因为此纯文本文件是此数据集的实际数据文件。</b>