The lymphatic and the blood vasculature are closely related systems that collaborate to ensure the organism’s physiological function. Despite their common developmental origin, they present distinct functional fates in adulthood that rely on robust lineage-specific regulatory programs. The recent technological boost in sequencing approaches unveiled long noncoding RNAs (lncRNAs) as prominent regulatory players of various gene expression levels in a cell-type-specific manner. To investigate the potential roles of lncRNAs in vascular biology, we performed antisense oligonucleotide (ASO) knockdowns of lncRNA candidates specifically expressed either in human lymphatic or blood vascular endothelial cells (LECs or BECs) followed by Cap Analysis of Gene Expression (CAGE-Seq). Here, we describe the quality control steps adopted in our analysis pipeline before determining the knockdown effects of three ASOs per lncRNA target on the LEC or BEC transcriptomes. In this regard, we especially observed that the choice of negative control ASOs can dramatically impact the conclusions drawn from the analysis depending on the cellular background. In conclusion, the comparison of negative control ASO effects on the targeted cell type transcriptomes highlights the essential need to select a proper control set of multiple negative control ASO based on the investigated cell types.

中文翻译：

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阴性对照反义寡核苷酸的选择会根据细胞背景显着影响下游分析

淋巴管和血液脉管系统是密切相关的系统，它们相互协作以确保机体的生理功能。尽管它们具有共同的发育起源，但它们在成年期呈现出不同的功能命运，这依赖于强大的谱系特异性监管计划。最近测序方法的技术进步揭示了长链非编码 RNA (lncRNA) 作为细胞类型特异性方式的各种基因表达水平的主要调节参与者。为了研究 lncRNA 在血管生物学中的潜在作用，我们对在人淋巴或血管内皮细胞 (LECs 或 BECs) 中特异性表达的 lncRNA 候选者进行反义寡核苷酸 (ASO) 敲低，然后对基因表达进行 Cap 分析 (CAGE-Seq) . 这里，在确定每个 lncRNA 靶标的三个 ASO 对 LEC 或 BEC 转录组的击倒效应之前，我们描述了我们分析流程中采用的质量控制步骤。在这方面，我们特别观察到阴性对照 ASO 的选择会根据细胞背景显着影响分析得出的结论。总之，阴性对照 ASO 对靶向细胞类型转录组的影响的比较突出了根据所研究的细胞类型选择合适的多阴性对照 ASO 对照集的必要性。我们特别观察到，阴性对照 ASO 的选择会根据细胞背景显着影响分析得出的结论。总之，阴性对照 ASO 对靶向细胞类型转录组的影响的比较突出了根据所研究的细胞类型选择合适的多阴性对照 ASO 对照集的必要性。我们特别观察到，阴性对照 ASO 的选择会根据细胞背景显着影响分析得出的结论。总之，阴性对照 ASO 对靶向细胞类型转录组的影响的比较突出了根据所研究的细胞类型选择合适的多阴性对照 ASO 对照集的必要性。