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. 2014 May 27:1:140005.
doi: 10.1038/sdata.2014.5. eCollection 2014.

miRNA expression atlas in male rat

Keiichi Minami  1 , Takeki Uehara  2 , Yuji Morikawa  2 , Ko Omura  3 , Masayuki Kanki  3 , Akira Horinouchi  4 , Atsushi Ono  5 , Hiroshi Yamada  6 , Yasuo Ohno  7 , Tetsuro Urushidani  8
Affiliations

miRNA expression atlas in male rat

Keiichi Minami et al. Sci Data. .

Abstract

MicroRNAs (miRNAs) are small (~22 nucleotide) noncoding RNAs that play pivotal roles in regulation of gene expression. The value of miRNAs as circulating biomarkers is now broadly recognized; such tissue-specific biomarkers can be used to monitor tissue injury and several pathophysiological conditions in organs. In addition, miRNA profiles of normal organs and tissues are important for obtaining a better understanding of the source of modulated miRNAs in blood and how those modulations reflect various physiological and toxicological conditions. This work was aimed at creating an miRNA atlas in rats, as part of a collaborative effort with the Toxicogenomics Informatics Project in Japan (TGP2). We analyzed genome-wide miRNA profiles of 55 different organs and tissues obtained from normal male rats using miRNA arrays. The work presented herein represents a comprehensive dataset derived from normal samples profiled in a single study. Here we present the whole dataset with miRNA profiles of multiple organs, as well as precise information on experimental procedures and organ-specific miRNAs identified in this dataset.

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Conflict of interest statement

The authors declare no competing financial interests.

Figures

Figure 1
Figure 1
Effect of circulating blood on miRNA expression in organs. Arrows indicate blood specific miRNAs; red arrows: miR-451, blue arrows: miR-144. Horizontal axis: Perfusion (-), vertical axis: Perfusion (+). Correlation coefficient (R 2 ); (a) Liver: 0.9998, (b) Kidney: 0.9960, (c) Lung: 0.9956, (d) Heart, atrium: 0.9988, (e) Heart, interventricular septum: 0.9994.
Figure 2
Figure 2
Principal component analysis (PCA). (a) PCA for all organ miRNAs. Spot colors represent broad types of organs; blue: nervous system, red: intestines, green: smooth or skeletal muscles, pink: lymphoid or hematopoietic system, light blue: reproductive system. Eigenvalues for each component: 29.1% (PC1), 11.4% (PC2); 8.1% (PC3), 6.7% (PC4), 5.0% (PC5). (b) PCA for digestive organs, nervous system or muscles. Eigenvalues for each component: (i) 37.2% (PC1), 10.8% (PC2); (ii) 35.7% (PC1), 13.2% (PC2); (iii) 31.0% (PC1), 16.4% (PC2).
Figure 3
Figure 3
Two-dimensional hierarchical clustering analysis based on the expression profiles of the 128 filtered probes. Horizontal: individual organs, vertical: miRNAs. In this analysis, expression profiles for the 128 probes filtered by model-based clustering were used for clustering.
Figure 4
Figure 4
Expression profiles of organ-specific miRNAs identified in this study. Horizontal: individual organs, vertical: normalized signal intensity. Each bar represents mean±S.D. (Organ ID 1–5: N=6, organ ID 6–55: N=3).
See this image and copyright information in PMC

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References

Data Citations

    1. Minami K., Uehara T. 2013. Gene Expression Omnibus. GSE52754

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