来一个示例吧,这篇文章(Long noncoding RNAs expression patterns associated with chemo response to cisplatin based chemotherapy in lung squamous cell carcinoma patients. PLoS One 2014; PMID: 25250788) 使用的是 GPL16956 Agilent-045997 Arraystar human lncRNA microarray V3 (Probe Name Version)
Compared with the PD samples, 953 lncRNAs were consistently upregulated and 749 lncRNAs were downregulated consistently among the differentially expressed lncRNAs in PR samples (Fold Change≥2.0-fold, p <0.05).
比如 GSE60689 Identification of LncRNA Expression Signatures for Triple-negative Breast Cancer , 文章是 lncRNA directs cooperative epigenetic regulation downstream of chemokine signals. Cell 2014 Nov PMID: 25416949 , 仅仅是4个样本,两个分组。
GSM1485226 Normal adjacent breast tissue [73] GSM1485227 Infiltrating Ductal Carcinima of breast [73] GSM1485228 Infiltrating Ductal Carcinima of breast [67] GSM1485229 Normal adjacent breast tissue [67]
但是该做的分析一点都不会少,仍然是 Scatter plots of lncRNAs significantly up-regulated (red) or down-regulated (green) in two pairs of TNBC tissues compared to the matched adjacent normal tissues (NBT).
看数据集:GSE46896,其文章发表在一个很普通的杂志:Biol Reprod. 2013 Nov 7; 标题是:Expression profiling reveals developmentally regulated lncRNA repertoire in the mouse male germline 实验设计的很好,主要是分析太简陋了,生物学故事很一般。而且全文绘图都是Excel表格样式:
In an attempt to identify the regulatory networks of mRNA and ncRNAs in GC, six pairs of GC tissues and non-tumorous adjacent tissues were analyzed via microarray using the Human LncRNA+mRNA Array v3.0 together with the miRCURY LNATM microRNA Array.
类似的LncRNA + mRNA array 研究非常多,再比如文章:Long noncoding RNA expression profile reveals lncRNAs signature associated with extracellular matrix degradation in kashin-beck disease
LncRNA and mRNA expression profiling were performed using Agilent human lncRNA + mRNA array 4.0 platform (4 × 180 K), with each array containing approximately 41,000 lncRNA and 34,000 mRNA probes.
In this study, we identified 316 up-regulated and 631 down-regulated lncRNAs (≥ 2-fold change) in KBD chondrocytes
We also identified 232 up-regulated and 427 down-regulated mRNAs (≥ 2-fold change).