Specimens

Pools of 6 rat pineal glands were collected at mid-day (ZT7) and mid-night (ZT19) from animals housed in a 14:10 light:dark lighting cycle. In addition, a mixed tissue sample was prepared from material collected from three rats at ZT7. The tissues were: cortex, cerebellum, midbrain, hypothalamus, hindbrain, spinal cord, retina, pituitary, heart, liver, lung, kidney, skeletal muscle, small intestine, adrenal gland.

RNA Preparation

Samples of tissue from the three animals were mixed. Total RNA was extracted using an RNeasy Kit with on-column DNase treatment. To prepare the mixed tissue sample, equal amounts of RNA from each of the 15 tissues were combined.

RNA-Seq library preparation and sequencing

Total RNA (10 ug) from the pineal gland pools and mixed tissue samples was ribosomal RNA-depleted (=ribo), fragmented and sequenced on an Illumina GAII machine, yielding paired-end 51-mer reads.

Note: In some cases, the mixed tissue values for selected genes are exceptionally high because that gene is very highly expressed in only one tissue, e.g., Rho and GH are strongly expressed only in the retina and pituitary gland, respectively.

Bioinformatics methods

See bioinformatics methods for details.