Gene expression differences between Gata2cko and wt mouse midbrain

Transcription factor Gata2 has been shown to regulate the development of the GABAergic neurons in the mouse midbrain. To gain information about the possible target genes of the Gata2 transcription factor, we used cDNA microarrays to compare gene expression in the embryonic day 12.5 (E12.5) wild-type and Gata2 mutant embryos. In this dataset, gene expression in control and Gata2cko dorsal and ventral midbrain tissues is reported. The ventral_mb_mut_rep3 sample was identified as outlier in sample correlation analysis and excluded from the differential gene expression analysis. The samples 13-18 are part of the GEO dataset GSE89354:GSM2367121-GSM2367126. Dorsal midbrain and ventral midbrain regions of the neural tube were dissected from the E12.5 mouse embryos from the En1-cre, Gata2 flox/+ x Gata2 flox/flox crosses. Tissue pieces were frozen in liquid nitrogen. After genotyping, dissected samples were pooled according to genotype, combining 6 En1-cre, Gata2 flox/+ samples into one control pool, and 6 En1-cre, Gata2 flox/flox samples into one mutant pool. Separate sample pools were prepared from dorsal midbrain and ventral midbrain samples. RNA was extracted with TriZol, from 3 independent sample pools (biological replicates) per genotype. Extracted RNA was reverse transcribed and labelled according to standard Illumina protocols and hybridized on Illumina Mouse WG-6 Expression BeadChip arrays. For the comparison of gene expression, relicates were grouped according to genotype (control vs mutant).转录因子Gata2（Transcription factor Gata2）已被证实可调控小鼠中脑γ-氨基丁酸能神经元（GABAergic neurons）的发育。为获取Gata2转录因子的潜在靶基因信息，我们采用cDNA微阵列（cDNA microarrays）对比了胚胎第12.5天（E12.5）野生型与Gata2突变型小鼠胚胎的基因表达谱。本数据集收录了对照组及Gata2cko小鼠背侧、腹侧中脑组织的基因表达数据。其中ventral_mb_mut_rep3样本在样本相关性分析中被鉴定为异常值，已被排除出差异基因表达分析流程。样本13-18隶属于基因表达综合数据库（Gene Expression Omnibus, GEO）数据集GSE89354:GSM2367121-GSM2367126。研究人员从En1-cre、Gata2 flox/+与Gata2 flox/flox杂交繁育的E12.5小鼠胚胎中，分离神经管的背侧中脑与腹侧中脑区域，将组织块置于液氮中快速冷冻。完成基因分型后，根据基因型对解剖获取的样本进行混样：将6份En1-cre、Gata2 flox/+样本整合为1份对照混样，将6份En1-cre、Gata2 flox/flox样本整合为1份突变型混样。分别针对背侧中脑与腹侧中脑样本制备独立的样本混样。每个基因型设置3个独立的样本混样作为生物学重复（biological replicates），采用TriZol试剂提取总RNA。提取得到的RNA按照标准Illumina实验流程进行反转录与标记，并在Illumina小鼠全基因组表达微珠芯片（Illumina Mouse WG-6 Expression BeadChip arrays）上完成杂交。在基因表达比较分析中，重复样本按基因型分为对照组与突变型两组进行对比。