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Gene. 2016 Jan 15;576(1 Pt 3):560-70. doi: 10.1016/j.gene.2015.11.003. Epub 2015 Nov 6.

Identification and analysis of house-keeping and tissue-specific genes based on RNA-seq data sets across 15 mouse tissues.

Author information

1
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.
2
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China.
3
Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, Riyadh 11442, Saudi Arabia.
4
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China; Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, Riyadh 11442, Saudi Arabia. Electronic address: liuwf@big.ac.cn.
5
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China. Electronic address: husn@big.ac.cn.

Abstract

Recently, RNA-seq has become widely used technology for transcriptome profiling due to its single-base accuracy and high-throughput speciality. In this study, we applied a computational approach on an integrated RNA-seq dataset across 15 normal mouse tissues, and consequently assigned 8408 house-keeping (HK) genes and 2581 tissue-specific (TS) genes among UCSC RefGene annotation. Apart from some basic genomic features, we also performed expression, function and pathway analysis with clustering, DAVID and Ingenuity Pathway Analysis, indicating the physiological connections (tissues) and diverse biological roles of HK genes (fundamental processes) and TS genes (tissue-corresponding processes). Moreover, we used RT-PCR method to test 18 candidate HK genes and finally identified a novel list of highly stable internal control genes: Ywhae, Ddb 1, Eif4h, etc. In summary, this study provides a new HK gene and TS gene resource for further genetic and evolution research and helps us better understand morphogenesis and biological diversity in mouse.

KEYWORDS:

Housekeeping; Mouse; RNA sequencing; Real-time PCR; Tissue specificity; Transcriptome profiling

PMID:
26551299
DOI:
10.1016/j.gene.2015.11.003
[Indexed for MEDLINE]

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