Use of multiple time points to model parotid differentiation.

Use of multiple time points to model parotid differentiation.
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使用多个时间点来模拟腮腺分化。

DOI：
10.1016/j.gdata.2015.05.005
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发表时间：
2015
期刊：
Genomics data
影响因子：
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通讯作者：
Darling,DouglasS
Darling,DouglasS
中科院分区：
--
文献类型：
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作者：
Metzler,MelissaA;Appana,Savitri;Brock,GuyN;Darling,DouglasS

文献摘要

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为了了解唾液腺泡细胞的终末分化过程，在大鼠腮腺中长达一个月的分化过程中测量mRNA和microRNA表达。使用激光捕获显微切割（LCM）在9个时间点（mRNA）或4个时间点（microRNA）一式三份分离腺泡细胞。该数据集的值之一来自本研究中使用的高质量RNA（RIN > 7），其可能难以从这样的富含RNaseI的组织获得。通过大鼠基因组微阵列杂交（www.ncbi.nlm.nih.gov/geo/query/acc.cgi? acc= GSE 65586），以及通过qPCR阵列（www.ncbi.nlm.nih.gov/geo/query/acc.cgi? acc= GSE 65324）。比较不同年龄组的表达情况，发现2656个mRNA和64个microRNA存在差异表达。由于mRNA表达在许多时间点取样，聚类和回归分析能够识别以前未涉及腺泡分化的动态表达模式。两个数据集的整合允许识别microRNA靶基因和基因调控网络。提供了生物信息学R代码以及实验方法和数据分析的其他细节。
In order to understand the process of terminal differentiation in salivary acinar cells, mRNA and microRNA expression was measured across the month long process of differentiation in the parotid gland of the rat. Acinar cells were isolated at either nine time points (mRNA) or four time points (microRNA) in triplicate using laser capture microdissection (LCM). One of the values of this dataset comes from the high quality RNA (RIN > 7) that was used in this study, which can be prohibitively difficult to obtain from such an RNaseI-rich tissue. Global mRNA expression was measured by rat genome microarray hybridization (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65586), and expression of microRNAs by qPCR array (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65324). Comparing expression at different ages, 2656 mRNAs and 64 microRNAs were identified as differentially expressed. Because mRNA expression was sampled at many time points, clustering and regression analysis were able to identify dynamic expression patterns that had not been implicated in acinar differentiation before. Integration of the two datasets allowed the identification of microRNA target genes, and a gene regulatory network. Bioinformatics R code and additional details of experimental methods and data analysis are provided.