Whole transcriptome profiling of the rat pineal gland using mid-day and mid-night samples (Experiment 3)
The rat pineal transcriptome is highly dynamic, with many hundreds of transcripts changing more than two-fold on a 24-hr basis, 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 pineal glands at mid-day (ZT7) and at mid-night (ZT19) from animals that were housed in a 14:10 light:dark lighting cycle. We also wished to identify transcripts that were selectively expressed in the pineal glands relative to other tissues; to do this, RNA was sequenced from a pool of 15 different tissues collected from 3 animals at mid-day (ZT7). PolyA-selected RNA was fragmented and sequenced on an Illumina HiSeq 2000 machine, yielding paired-end, 101-mer reads. This is Experiment 3 of several 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 Experiments 1 through 4 are included in Coon et al., 2012 and have been archived as separate SRA entries: Experiment 1, SRA037284; Experiment 2, SRA052823; Experiment 4, SRA053154.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.  The transcriptome of a sample of mixed tissues was also sequenced for comparison to aid in determining pineal-enriched transcripts.