The role of Lhx4 and Bsx homeobox genes in the rat adult pineal gland

Homeobox genes generally encode transcription factors involved in regulating developmental processes. In the pineal gland, a brain structure devoted to nocturnal melatonin synthesis, a number of homeobox genes are also expressed postnatally; among these are the LIM homeobox 4 gene (Lhx4) and the brain-specific homeobox gene (Bsx). As part of a larger study, we used of siRNA technology to knock down Lhx4 or Bsx expression in cultured adult rat pinealocytes. For RNAseq, nine barcoded libraries were pooled and sequenced on one Flow Cell of a HiSeq2500 (Illumina) in Rapid Run Mode yielding a total of 410 million 2·x 100-bp read-pairs (average reads per sample: 45.6·106 ± 3.3·106 SEM). Analysis of control and siRNA-treated pinealocytes revealed downstream target genes and insights into the role these homeobox genes play in the adult pineal gland. The two processed data file present siLhx4 vs siNT, or siBsx vs siNT. Overall design: There are nine sample total of RNA extracted from adult rat pinealocytes treated with short-interfering RNAs (siRNA). There are triplicates of Control nontargeting siRNA (siNT), siRNA targeting Lhx4 (siLhx4), or siRNA targeting Bsx (siBsx).