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Title: Database for mRNA Half-Life of 19,977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse      
keywords:
Transcriptome or Gene expression
ID:
PRJNA110631
description:
Degradation of mRNA is one of the key processes that control the steady-state level of gene expression. However, the rate of mRNA decay for the majority of genes is not known. We successfully obtained the rate of mRNA decay for 19 977 non-redundant genes by microarray analysis of RNA samples obtained from mouse embryonic stem (ES) cells. Median estimated half-life was 7.1 h and only <100 genes, including Prdm1, Myc, Gadd45 g, Foxa2, Hes5 and Trib1, showed half-life less than 1 h. In general, mRNA species with short half-life were enriched among genes with regulatory functions (transcription factors), whereas mRNA species with long half-life were enriched among genes related to metabolism and structure (extracellular matrix, cytoskeleton). The stability of mRNAs correlated more significantly with the structural features of genes than the function of genes: mRNA stability showed the most significant positive correlation with the number of exon junctions per open reading frame length, and negative correlation with the presence of PUF-binding motifs and AU-rich elements in 30 -untranslated region (UTR) and CpG di-nucleotides in the 50 -UTR. The mRNA decay rates presented in this report are the largest data set for mammals and the first for ES cells. Keywords: growth condition design,reference design,replicate design,RNA stability design,time series design Overall design: We used two mouse ESC lines: MC1 derived from mouse strain 129S6/SvEvTac and MC2-B6 derived from strain C57BL/6J. To remove contaminating feeder cells, ES cells were first cultured for two passages on gelatin-coated culture dish in complete ES medium. Differentiated ES cells were obtained from MC1 cells by LIF withdrawal (complete medium without LIF, below referenced as LIF-) or by retinoic acid (RA) treatment. To measure mRNA stability, transcription was blocked by adding actinomycin D to the medium. RNA was hybridized in duplicate for each cell type and time point. All hybridizations were carried out by combining a Cy3-CTP-labeled experimental target and a Cy5-CTP-labeled Universal Mouse Reference target.
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landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA110631
authentication:
none
authorization:
none
ID:
pmid:19001483
name:
Mus musculus
ncbiID:
ncbitax:10090
abbreviation:
NCBI
homePage: http://www.ncbi.nlm.nih.gov
ID:
SCR:006472
name:
National Center for Biotechnology Information
homePage: http://www.ncbi.nlm.nih.gov/bioproject
ID:
SCR:004801
name:
NCBI BioProject