Differential Expression of Coding and Long Noncoding RNAs in Keratoconus-Affected Corneas
Differential Expression of Coding and Long Noncoding RNAs in Keratoconus-Affected Corneas
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DOI：
10.1167/iovs.18-24267
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发表时间：
2018-06-01
影响因子：
4.4
通讯作者：
Liu, Yutao
中科院分区：
文献类型：
--
作者：
Khaled, Mariam Lofty;Bykhovskaya, Yelena;Liu, Yutao
目的。圆锥角膜（KC）是最常见的角膜扩张症。我们的目的是确定受 KC.METHODS 影响的人角膜中编码和长非编码 RNA (lncRNA) 的差异表达。从 10 名 KC 患者和 8 名非 KC 健康对照的角膜中，去除核糖体 RNA 后，使用 SMARTer Stranded RNA-Seq 试剂盒制备 200 ng 总 RNA 测序文库，然后使用 Ilitunina 测序仪进行双端 50 bp 测序。使用 TopHat/Cufflinks 以及来自 Ensembl 的基因文件和来自 NONCODE 的 IncRNA 文件进行差异分析。使用 WebGestalt 进行路径分析。利用每个样本中差异表达的编码和非编码RNA的表达水平，我们分别将它们在KC和对照中的表达水平相关联，并识别出KC与对照中显着不同的相关性，然后使用Cytoscape进行可视化。结果。使用“倍数变化”> = 2 和错误发现率
PURPOSE. Keratoconus (KC) is the most common corneal ectasia. We aimed to determine the differential expression of coding and long noncoding RNAs (lncRNAs) in human corneas affected with KC.METHODS. From the corneas of 10 KC patients and 8 non-KC healthy controls, 200 ng total RNA was used to prepare sequencing libraries with the SMARTer Stranded RNA-Seq kit after ribosomal RNA depletion, followed by paired-end 50-bp sequencing with Ilitunina Sequencer. Differential analysis was done using TopHat/Cufflinks with a gene file from Ensembl and a IncRNA file from NONCODE. Pathway analysis was performed using WebGestalt. Using the expression level of differentially expressed coding and noncoding RNAs in each sample, we correlated their expression levels in KC and controls separately and identified significantly different correlations in KC against controls followed by visualization using Cytoscape.RESULTS. Using 'fold change' >= 2 and a false discovery rate