A Resource for Transcriptomic Analysis in the Mouse Brain
A Resource for Transcriptomic Analysis in the Mouse Brain
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DOI：
10.1371/journal.pone.0003012
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发表时间：
2008-08-20
期刊：
影响因子：
3.7
通讯作者：
Carninci, Piero
中科院分区：
文献类型：
--
作者：
Plessy, Charles;Fagiolini, Michela;Carninci, Piero
背景：大脑皮层的转录组是非常同质的，个体之间的差异比区域之间的差异更大。人们认为，由于存在许多不同的细胞类型，一个细胞群体内的差异将与来自其他细胞群体的噪声进行平均。分选细胞表达相同的转基因的研究表明，细胞群体可以区分根据其transcriptionprofile.Methodology：我们已经准备了一个低冗余集的16,209全长cDNA克隆，代表小鼠视觉皮层的转录组在其编码和非编码方面。使用一个独立的标签为基础的方法，CAGE，我们证实了72%的克隆的皮质表达。通过PCR扩增克隆，并点在玻璃载玻片上，我们询问的微阵列与RNA流分选荧光细胞从大脑皮层的parvalbumin-EGFP转基因mice.Conclusions：我们提供了一个注释的cDNA克隆收集，这是特别适合于在小鼠大脑中的转录组学分析。将其点在微阵列上，我们比较了在小白蛋白-EGFP转基因背景中EGFP阳性和阴性细胞的转录组，并显示超过30%的克隆差异表达。我们的克隆收集将是一个有用的资源，在大脑皮层的单细胞类型的转录组的研究。
Background: The transcriptome of the cerebral cortex is remarkably homogeneous, with variations being stronger between individuals than between areas. It is thought that due to the presence of many distinct cell types, differences within one cell population will be averaged with the noise from others. Studies of sorted cells expressing the same transgene have shown that cell populations can be distinguished according to their transcriptional profile.Methodology: We have prepared a low-redundancy set of 16,209 full-length cDNA clones which represents the transcriptome of the mouse visual cortex in its coding and non-coding aspects. Using an independent tag-based approach, CAGE, we confirmed the cortical expression of 72% of the clones. Clones were amplified by PCR and spotted on glass slides, and we interrogated the microarrays with RNA from flow-sorted fluorescent cells from the cerebral cortex of parvalbumin-egfp transgenic mice.Conclusions: We provide an annotated cDNA clone collection which is particularly suitable for transcriptomic analysis in the mouse brain. Spotting it on microarrays, we compared the transcriptome of EGFP positive and negative cells in a parvalbumin-egfp transgenic background and showed that more than 30% of clones are differentially expressed. Our clone collection will be a useful resource for the study of the transcriptome of single cell types in the cerebral cortex.