Whole transcriptome profiling of the rat pineal gland using mid-day and mid-night samples (Experiment 2)
The transcriptome of the rat pineal gland is highly dynamic, with many hundreds of genes changing more than two-fold on a 24-hr daily rhythm, as revealed earlier using Affymetrix GeneChip analysis. We sought to more completely characterize this temporally dynamic transcriptome using RNA-Seq to capture information regarding alternative splicing, novel exons, unannotated mRNAs, non-coding RNAs and coding transcripts not represented on the Affymetrix chips.  Toward this end we performed RNA-Seq on pools of rat  pineal glands obtained  at  mid-day (ZT7) and mid-night (ZT19).   Animals had been housed in a 14:10 light:dark lighting cycle. PolyA-selected RNA was fragmented and sequenced on an Illumina HiSeq 2000 machine, yielding paired-end, 101-mer reads. This is Experiment 2 of similar RNA-Seq experiments investigating the rat pineal transcriptome at ZT7 compared to ZT19. Experiments 1 through 4 are included in Coon et al., 2012 and have been archived as separate SRA entries: Experiment 1, SRA037284; Experiment 3, SRA052826; Experiment 4, SRA053154.
The rat pineal transcriptome was sequenced using mid-day and mid-night samples to describe the pineal transcriptome and to identify transcripts that exhibit day/night differences in expression.