Differentially regulated genes E14.5 spial cord NFIX KO vs WT

The rationale behind this profiling experiment was to understand transcriptional changes arising in the developing spinal cord in the absence of <i>Nfix. </i>To do this, <i>Nfix^-/-</i> mice and their wild-type littermates were used in this study. These mice were maintained on a C57Bl/6J genetic background. Heterozygous male and female mice were placed together overnight to produce time-mated litters. The presence of a vaginal plug the following day indicated a successful mating was likely, and this was designated E0.5. Pregnant dams were euthanized by cervical dislocation. Embryos were removed and placed on ice. Whole spinal cords were dissected from E14.5 <i>Nfix^-/-</i> and wild-type mouse embryos and snap frozen using dry ice. An RNeasy Micro Kit (QIAGEN) was used to extract total RNA from these samples, which were then diluted to 80 ng/μL and sent to the Ramaciotti Centre (University of New South Wales, Australia) for microarray analysis on a Mouse Transcriptome Array 2.0ST (Affymetrix). Raw microarray data in the form of .CEL files were received from the Ramaciotti Centre and initially processed by running an SST-RMA (gene level) analysis on all samples using the Affymetrix Expression Console software (build 1.4.1.46). The resulting .CHP files were then imported into the Affymetrix Transcription Analysis Console (TAC) software and sample files were compared in differential gene expression analyses between <i>Nfix^-/-</i> and wild-type samples. Algorithm parameters selected included: genome version mm10, one-way between-subject ANOVA (unpaired) and ANOVA <i>p</i>-value (condition pair) &lt;0.05. Differential gene expression analyses were performed using Affymetrix Transcription Analysis Console (TAC) software. Gene expression levels between <i>Nfix^-/-</i> and wild-type samples were compared using a one-way between-subject ANOVA (unpaired) and corrected for FDR. A <i>p-</i>value &lt;0.05 denoted a statistically significant difference in gene expression between samples. A fold change cut-off for differential expression of &gt; ± 1.5 was also used to stratify differentially expressed genes.