Pozhitkov Alexander E, Noble Peter A
City of Hope, Information Sciences-Beckman Research Institute, Irwindale, CA.
Max-Planck-Institute for Evolutionary Biology, Ploen, Germany.
Commun Integr Biol. 2017 Sep 6;10(4):e1329785. doi: 10.1080/19420889.2017.1329785. eCollection 2017.
We previously reported that thousands of transcripts in the mouse and zebrafish significantly increased in abundance in a time series spanning from life to several days after death. Transcript abundances were determined by: calibrating each microarray probe using a dilution series of pooled RNAs, fitting the probe-responses to adsorption models, and back-calculating abundances using the probe signal intensity of a sample and the best fitting model. The accuracy of the abundance measurements was not assessed in our previous study because individual transcript concentrations in the calibration pool were not known. Accurate transcript abundances are highly desired for modeling the dynamics of biological systems and investigating how systems respond to perturbations. In this study, we show that accurate transcript abundances can be determined by calibrating the probes using a calibration pool of transcripts with known concentrations. Instructions for determining accurate transcript abundances using the Gene Meter approach are provided.
我们之前报道过，在从小鼠和斑马鱼出生到死后数天的时间序列中，数千种转录本的丰度显著增加。转录本丰度的确定方法如下：使用混合RNA的稀释系列校准每个微阵列探针，将探针响应拟合到吸附模型，并使用样品的探针信号强度和最佳拟合模型反算丰度。在我们之前的研究中未评估丰度测量的准确性，因为校准池中单个转录本的浓度未知。准确的转录本丰度对于构建生物系统动力学模型以及研究系统如何响应扰动非常重要。在本研究中，我们表明可以通过使用已知浓度的转录本校准池来校准探针，从而确定准确的转录本丰度。本文提供了使用基因计量法确定准确转录本丰度的说明。
