Study SRP013378 Download

TitleWhole transcriptome profiling of the rat pineal gland using mid-day and mid-night samples (Experiment 4)
AbstractThe 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. This sequencing experiment generated strand-specific RNA-Seq data to differentiate transcripts from opposite genomic strands.
Referencesno content
OrganismsRattus norvegicus
TypeTranscriptome Analysis
DescriptionThe 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 Experiments 1 through 4 are included in Coon et al., 2012 and have been archived as separate SRA entries: Experiment 1, SRA037284; Experiment 2, SRA052823; Experiment 3, SRA052826.
SubmitterNIH-NICHD-David Klein
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