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).