Baseline mRNA expression differs widely between common laboratory strains of zebrafish.
Baseline mRNA expression differs widely between common laboratory strains of zebrafish.
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DOI：
10.1038/s41598-018-23129-4
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发表时间：
2018-03-19
影响因子：
4.6
通讯作者：
Brown KH
中科院分区：
文献类型：
--
作者：
Holden LA;Brown KH
野生斑马鱼（Danio rerio）的常见菌株具有独特的基因组特征，包括snp和CNV，但菌株信息往往未在文献中报道。因此，品系间变异的混淆效应使得在斑马鱼中重复研究具有挑战性。在这里，我们使用安捷伦4 × 44 K基因表达芯片分析了三种常见斑马鱼菌株（AB、Tuebingen （TU）和WIK）的肝脏mRNA表达模式，以建立菌株之间和性别之间的基线mRNA表达。我们观察到AB和WIK菌株的性别特异性基因表达差异很大（AB有141个基因，WIK有67个基因），但TU菌株的性别差异不显著。在将数据集划分为雄性和雌性亚群后，我们检测到421个独特的mRNA转录本，差异表达具有统计学意义；269个mRNA转录本在雄性之间存在差异，212个mRNA转录本在雌性之间存在差异，59个mRNA转录本在三个菌株之间存在差异。mRNA表达谱在性别和菌株之间存在差异并不奇怪，但表征差异是必要的。这些结果突出了斑马鱼内部变异的复杂性，并强调了该模型系统作为其他物种（包括人类）正常变异的有效表征的价值。
Common strains of wildtype zebrafish (Danio rerio) have unique genomic features including SNPs and CNV, but strain information often goes unreported in the literature. As a result, the confounding effects of interstrain variation makes repetition of studies in zebrafish challenging. Here we analyze hepatic mRNA expression patterns between three common zebrafish strains (AB, Tuebingen (TU), and WIK) using Agilent 4 × 44 K gene expression microarrays to establish baseline mRNA expression across strains and between sexes. We observed wide variation in sex-specific gene expression within AB and WIK strains (141 genes in AB and 67 genes in WIK), but no significant variation between sexes within TU. After partitioning the dataset into male and female subsets, we detected 421 unique mRNA transcripts with statistically significant differential expression; 269 mRNA transcripts varied between males, 212 mRNA transcripts varied between females, and 59 mRNA transcripts varied across the three strains, regardless of sex. It is not surprising that mRNA expression profiles differ between sexes and strains, but it is imperative to characterize the differences. These results highlight the complexity of variation within zebrafish and underscore the value of this model system as a valid representation of normal variation present in other species, including humans.
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影响因子：
14.9
作者：
Pizarro A;Hayer K;Lahens NF;Hogenesch JB
通讯作者：
Hogenesch JB
影响因子：
3.3
作者：
Bowen, Margot E.;Henke, Katrin;Harris, Matthew P.
通讯作者：
Harris, Matthew P.
影响因子：
5.3
作者：
Bertolucci, Cristiano;Cavallari, Nicola;Pinotti, Mirko
通讯作者：
Pinotti, Mirko
影响因子：
2.7
作者：
Coe, T. S.;Hamilton, P. B.;Tyler, C. R.
通讯作者：
Tyler, C. R.
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y