Transcription profiling of mouse adult brain hemispheres

Inbred congenic strain B6.C6.132.54/Vad was created using C57BL/6ByJ background and BALB/cJ donor strains. Flanking background markers at chr. 6: 75.9 Mb (rs4226008, NCBI Mouse Build 36 / dbSNP Build 126) and 122.3 Mb (rs3023093), and limiting donor markers at 81.9 Mb (rs4226024) and at 91.8 Mb (rs3712161) defined the introgressed region. We concluded the segment size must be between 9.9 Mb and 46.4 Mb. In a Quantitative Trait Gene identification study we compared brain (without cerebellum) gene expression between progenitors and congenics. Such comparisons can facilitate identification of cis-regulated genes and to establish genetic control of a complex phenotype whose expression is associated with the introgressed chromosome segment. We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process. Experiment Overall Design: Experiments were carried out in three batches. In each batch 10 animals per strain were used. After processing each hemisphere separately, 10 hemispheres were pooled for one high-density oligonucleotide microarray (Mouse Genome 430 2.0, Affymetrix, Santa Clara, CA). For each strain 3 oligonucleotide microarrays were used (n=3). We used adult, untreated, male mice (n=30, 90 mice in toto).近交同源导入系（inbred congenic strain）B6.C6.132.54/Vad以C57BL/6ByJ作为遗传背景品系，以BALB/cJ为供体品系构建获得。6号染色体上75.9 Mb（rs4226008，NCBI小鼠基因组组装版本36 / dbSNP版本126）和122.3 Mb（rs3023093）处的侧翼背景遗传标记，以及81.9 Mb（rs4226024）、91.8 Mb（rs3712161）处的供体端限定遗传标记，共同界定了该染色体导入片段的区域。经测算，该导入片段的大小介于9.9 Mb至46.4 Mb之间。 在本项数量性状基因（Quantitative Trait Gene）鉴定研究中，我们对亲本品系与同源导入系的大脑（剔除小脑）基因表达谱开展了比较分析。此类比较可助力顺式调控基因的鉴定，并为解析与导入染色体片段表达相关的复杂表型的遗传调控机制提供支撑。我们通过基因芯片技术详细刻画了细胞化（cellularisation）进程背后的全局基因表达调控网络，并鉴定出该过程中多个类别的上调基因。 实验整体设计： 实验分为3个批次进行，每个批次中每个品系使用10只实验动物。将每个大脑半球单独处理后，取10个半球混合制备为一个样本，用于一张高密度寡核苷酸芯片（Mouse Genome 430 2.0，Affymetrix公司，美国加利福尼亚州圣克拉拉市）。每个品系使用3张寡核苷酸芯片（n=3）。本次实验采用未经任何处理的成年雄性小鼠，总样本量为90只（单组样本量n=30）。