Development of the prethalamus is crucial for thalamocortical projection formation and is regulated by Olig2

Thalamocortical axons pass through the prethalamus in the first step of their neural circuit formation Although it has been supposed that the prethalamus is an intermediate target for thalamocortical projection formation, much less is known about the molecular mechanisms of this targeting. The samples were grouped into 2 sample types: Olig2-KO and the wild-type. RNA was purified from the E13.5 ventral forebrain from Olig2-KO (Olig2-/-) and the wild-type (Olig2+/+). RNA samples were prepared by pooling RNAs extracted from 3 brains to constitute one replicate and each sample type was prepared in five replicates. cRNA hybridization probes were hybridized to Affymetrix Mouse Whole Genome MOE430 2.0 arrays. The R-CRAN statistical language and Bioconductor software package (Gentleman et al., 2004) were used throughout the expression analyses. Raw image files were processed using Affymetrix GCOS and the Microarray Suite (MAS) 5.0 algorithm. The probe signal levels were quantile-normalized, summarized and then transformed to the log 2 expression using GCRMA (gcrma R-package, Irizarry et al., 2003). Gene filtering was performed using the Wilcoxon signed-rank test to select probe sets that were "consistently expressed" (p <0.04) in at least one group (mas5calls R-package; Bioconductor). All samples showed good quality control according to MAS5.0 guidelines and the AffyQC report (R-package; Bioconductor).丘脑皮层轴突在神经环路形成的初始阶段会穿过前丘脑（prethalamus）。尽管此前学界普遍认为前丘脑是丘脑皮层投射形成的中间靶标，但针对该靶向过程的分子机制，目前人们的认知仍相对匮乏。本实验样本分为两类：Olig2敲除型（Olig2-KO）与野生型（wild-type）。研究人员分别从Olig2敲除型（Olig2-/-）与野生型（Olig2+/+）小鼠的胚胎13.5天腹侧前脑中提取并纯化RNA。每一份重复样本均混合3个小鼠脑组织提取的RNA制备而成，每类样本均设置5个生物学重复。将互补RNA（cRNA）杂交探针与Affymetrix小鼠全基因组MOE430 2.0芯片进行杂交。本研究的表达分析全程采用R-CRAN统计语言与Bioconductor软件包（Gentleman等人，2004）完成。原始图像文件通过Affymetrix GCOS软件与微阵列套件（MAS）5.0算法进行处理。探针信号强度经分位数归一化、汇总后，通过GCRMA算法（gcrma R包，Irizarry等人，2003）转换为以2为底的对数表达量。采用Wilcoxon符号秩检验开展基因筛选：通过mas5calls R包（Bioconductor）筛选出至少在一组样本中"consistently expressed"（p<0.04）的探针集。所有样本均符合MAS5.0质控指南与AffyQC报告（R包；Bioconductor）的质量控制标准。