Photoperiodism samples

Data sets

The photoperiodism dataset contains time-course samples of pars tuberalis (PT) in the adult mouse brain under the following 4 conditions.

short-day (SD)
mice under short-day (light : dark = 8hr : 16hr, ZT0 = lights on, ZT8 = lights off, 400lux) for 5 weeks
long-day (LD)
mice under short-day for 3 weeks and then under long-day (light : dark = 16hr : 8hr, ZT0 = lights on, ZT16 = lights off, 400lux) for 2 weeks
long-day advance (LD-advance)
mice advancing light-on timing by 8 hours (ZT16 = lights on, ZT8 = lights off) after 3 weeks short day, starting at the light-on timing (ZT16)
long-day delay (LD-delay)
mice delaying light-off timing by 8 hours (ZT0 = lights on, ZT16 = lights off) after 3-weeks short-day, starting at the light-on timing (ZT0)

For each condition, expression was profiled every 4 hours for 1 day. For each time point, there were two (n=2) biological replications. Thus, the database has 48 samples.


short-day and long-day conditions

Male CBA/N mice, which have normal retina, were purchased 3 weeks after birth. For chronic long-day and short-day experiments, the mice were first housed under short-day conditions, and were given food and water ad libitum and kept under these short-day conditions for 3 weeks. The mice were then separated into 2 groups. One group was maintained under the short-day conditions and the other was housed under long-day conditions for 2 weeks. Mice in both groups were sacrificed and their PTs were sampled every 4 hours for 1 day, starting at ZT0.

long-day advance and delay conditions

The mice were first housed under short-day conditions for 3 weeks as described above, and then separated into 2 groups. In one, the light-on timing was advanced by 8 hours, and in the other, the light-off timing was delayed by 8 hours. In both cases, photoperiod was extended by 8 hours. PTs from both groups were obtained every 4 hours for 1 day, starting at the lights-on timing (ZT16 in the advance condition and ZT0 in the delay condition, when ZT was defined in the short-day condition).


Slices (0.5-mm thick) of the brain of CBA/N mice were cut, frozen, and the PT was punched out with a microdissecting needle (gauge 0.5 mm) under a stereomicroscope. The samples included a small amount of the surrounding tissue, such as the median eminence and ependymal cells. We sampled 25 mice at each time point. This whole procedure was repeated twice (n = 2) to obtain experimental replicates.

The total RNA was prepared from the pooled PT samples obtained at each time point under each condition, using Trizol reagent (Gibco BRL). The cDNA synthesis and cRNA labelling reactions were performed as previously described. Affymetrix high-density oligonucleotide arrays for Mus musculus (GeneChip Mouse Genome 430 2.0) were hybridized, stained, and washed according to the Expression Analysis Technical Manual (Affymetrix). The expression values were summarized by the RMA method.

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