Abstract:
BACKGROUND:Gene expression analyses demand appropriate reference genes (RGs) for normalization, in order to obtain reliable assessments. Ideally, RG expression levels should remain constant in all cells, tissues or experimental conditions under study. Housekeeping genes traditionally fulfilled this requirement, but they have been reported to be less invariant than expected; therefore, RGs should be tested and validated for every particular situation. Microarray data have been used to propose new RGs, but only a limited set of model species and conditions are available; on the contrary, RNA-seq experiments are more and more frequent and constitute a new source of candidate RGs. RESULTS:An automated workflow based on mapped NGS reads has been constructed to obtain highly and invariantly expressed RGs based on a normalized expression in reads per mapped million and the coefficient of variation. This workflow has been tested with Roche/454 reads from reproductive tissues of olive tree (Olea europaea L.), as well as with Illumina paired-end reads from two different accessions of Arabidopsis thaliana and three different human cancers (prostate, small-cell cancer lung and lung adenocarcinoma). Candidate RGs have been proposed for each species and many of them have been previously reported as RGs in literature. Experimental validation of significant RGs in olive tree is provided to support the algorithm. CONCLUSION:Regardless sequencing technology, number of replicates, and library sizes, when RNA-seq experiments are designed and performed, the same datasets can be analyzed with our workflow to extract suitable RGs for subsequent PCR validation. Moreover, different subset of experimental conditions can provide different suitable RGs.
journal_name
Biomed Eng Onlinejournal_title
Biomedical engineering onlineauthors
Carmona R,Arroyo M,Jiménez-Quesada MJ,Seoane P,Zafra A,Larrosa R,Alché JD,Claros MGdoi
10.1186/s12938-017-0356-5subject
Has Abstractpub_date
2017-08-18 00:00:00pages
65issue
Suppl 1issn
1475-925Xpii
10.1186/s12938-017-0356-5journal_volume
16pub_type
杂志文章abstract::Herman P. Schwan [1915-2005] was a distinguished scientist and engineer, and a founding father of the field of biomedical engineering. A man of integrity, Schwan influenced the lives of many, including his wife and children, and his many students and colleagues. Active in science until nearly the end of his life, he w...
journal_title:Biomedical engineering online
pub_type: 传,历史文章,杂志文章
doi:10.1186/1475-925X-4-21
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abstract::Since falls are a major public health problem among older people, the number of systems aimed at detecting them has increased dramatically over recent years. This work presents an extensive literature review of fall detection systems, including comparisons among various kinds of studies. It aims to serve as a referenc...
journal_title:Biomedical engineering online
pub_type: 杂志文章,评审
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journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/1475-925X-4-54
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journal_title:Biomedical engineering online
pub_type: 杂志文章
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journal_title:Biomedical engineering online
pub_type: 杂志文章
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journal_title:Biomedical engineering online
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journal_title:Biomedical engineering online
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journal_title:Biomedical engineering online
pub_type: 杂志文章
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journal_title:Biomedical engineering online
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pub_type: 评论,信件
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pub_type: 杂志文章
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journal_title:Biomedical engineering online
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journal_title:Biomedical engineering online
pub_type: 杂志文章
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journal_title:Biomedical engineering online
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journal_title:Biomedical engineering online
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