Comparing RNA-Seq and microarray gene expression data in two zones of the Arabidopsis root apex relevant to spaceflight.
Comparing RNA-Seq and microarray gene expression data in two zones of the Arabidopsis root apex relevant to spaceflight.
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DOI：
10.1002/aps3.1197
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发表时间：
2018-11
影响因子：
3.6
通讯作者：
Paul AL
中科院分区：
文献类型：
--
作者：
Krishnamurthy A;Ferl RJ;Paul AL
根尖是参与环境感知的重要区域，但包括根的非常小的部分。因此，当样本有限时，获得根尖转录组具有挑战性。使用微小的根切片进行转录组分析的可行性进行了检查，比较RNA测序（RNA-Seq）和微阵列在表征与航天相关的基因方面的作用。 将拟南芥（Arabidopsis thaliana）哥伦比亚生态型（Col-0）根切成1区（0.5 mm;根冠和分生区）和2区（1.5 mm;过渡区、伸长区和生长终止区）。比较了两者的差异基因表达。微阵列和RNA-Seq都被证明适用于小样本。区1和区2之间总共有4180个基因差异表达（倍数变化为2或更大）。此外，通过RNA-Seq鉴定了771个独特基因和19个新的转录活性区域，这些基因在微阵列中未检测到。然而，微阵列检测到了在RNA-Seq中缺失的航天相关基因。单根尖子部分可用于使用RNA-Seq或微阵列的转录组分析。RNA测序和微阵列都提供了新的信息。这些数据表明，处理来自太空飞行的小而稀有样本的技术可以进一步增强，并且RNA测序可能会错过一些与太空飞行相关的基因表达变化。
The root apex is an important region involved in environmental sensing, but comprises a very small part of the root. Obtaining root apex transcriptomes is therefore challenging when the samples are limited. The feasibility of using tiny root sections for transcriptome analysis was examined, comparing RNA sequencing (RNA‐Seq) to microarrays in characterizing genes that are relevant to spaceflight. Arabidopsis thaliana Columbia ecotype (Col‐0) roots were sectioned into Zone 1 (0.5 mm; root cap and meristematic zone) and Zone 2 (1.5 mm; transition, elongation, and growth‐terminating zone). Differential gene expression in each was compared. Both microarrays and RNA‐Seq proved applicable to the small samples. A total of 4180 genes were differentially expressed (with fold changes of 2 or greater) between Zone 1 and Zone 2. In addition, 771 unique genes and 19 novel transcriptionally active regions were identified by RNA‐Seq that were not detected in microarrays. However, microarrays detected spaceflight‐relevant genes that were missed in RNA‐Seq. Single root tip subsections can be used for transcriptome analysis using either RNA‐Seq or microarrays. Both RNA‐Seq and microarrays provided novel information. These data suggest that techniques for dealing with small, rare samples from spaceflight can be further enhanced, and that RNA‐Seq may miss some spaceflight‐relevant changes in gene expression.
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影响因子：
5.3
作者：
Paul AL;Zupanska AK;Schultz ER;Ferl RJ
通讯作者：
Ferl RJ
影响因子：
4.5
作者：
Bruex A;Kainkaryam RM;Wieckowski Y;Kang YH;Bernhardt C;Xia Y;Zheng X;Wang JY;Lee MM;Benfey P;Woolf PJ;Schiefelbein J
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Schiefelbein J
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作者：
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通讯作者：
Hochholdinger, Frank
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6.9
作者：
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通讯作者：
Rashotte AM
影响因子：
4.3
作者：
BALUSKA, F;KUBICA, S;HAUSKRECHT, M
通讯作者：
HAUSKRECHT, M