Transcription profiling of mouse ADNP knockout vs wild type

The putative transcription factor, activity-dependent neuroprotective protein (ADNP) is a zinc finger and homeodomain-like profile containing protein. ADNP knockout mice die at day 9 of gestation. To reveal ADNP-associated pathways, a 22,690- Affymetrix probe array was used on ADNP knockout and control embryos. Experiment Overall Design: To identify downstream target genes of ADNP, we examined global gene expression profiles of whole E9 knockout embryos (KO - ADNP -l-), their wild-type (WT - ADNP +l+ ) and their heterozygous (H - ADNP -l+ ) littermates, using the Affymetrix Murine Genome 430A oligonucleotide microarrays. Gestation day 9 was chosen as it is the period at which embryos lacking ADNP exhibit distinct morphological and developmental changes prior to degeneration and in uterus absorption. Total RNA was extracted from four ADNP knockout embryos, four normal embryos and six heterozygous embryos. A pool of two genotype identical littermates was used on seven different arrays (pooling of two embryos was necessary to obtain enough RNA on each of the gene microarrays).活性依赖性神经保护蛋白（ADNP）是一种推定的转录因子，属于包含锌指结构与同源结构域样基序的蛋白质。ADNP基因敲除小鼠会在妊娠第9天死亡。为揭示ADNP相关的信号通路，研究人员采用搭载22690个探针的Affymetrix探针阵列，对ADNP敲除胚胎与对照胚胎开展检测。实验总体设计：为鉴定ADNP的下游靶基因，研究人员采用Affymetrix小鼠基因组430A寡核苷酸微阵列，对胚胎发育第9天的完整ADNP敲除胚胎（KO - ADNP⁻/⁻）、同窝野生型胚胎（WT - ADNP⁺/⁺）以及杂合子胚胎（H - ADNP⁻/⁺）的全基因组基因表达谱进行了检测。选择妊娠第9天作为检测节点，是因为此时ADNP缺失胚胎在发生退行性变及宫内吸收前，已出现显著的形态学与发育学改变。研究人员从4枚ADNP敲除胚胎、4枚正常胚胎以及6枚杂合子胚胎中提取总RNA。将2只基因型一致的同窝胚胎样本混合后，在7张不同的微阵列芯片上进行检测（由于每张基因微阵列需要足量的RNA样本，因此需将2枚胚胎的材料混合以满足检测需求）。