Affymetrix GeneChip Rhesus Macaque Genome Array [Rhesus]

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Impact of moderate calorie restriction on the reproductive neuroendocrine axis of male rhesus macaques

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Transcription profiling of pituitary gland and testis of rhesus macaques fed a normal or moderately calorie restricted diet

Impact of moderate calorie restriction on the reproductive neuroendocrine axis of male rhesus macaques


Affymetrix:Protocol:Hybridization-Unknown

Affymetrix:Protocol:MAS4:ExpressionCall

Title: Affymetrix CHP Analysis (ExpressionCall). Description:

P-AFFY-2

Labeling of samples was carried out according to the manufacturer’s standard protocol

P-AFFY-6

Title: Affymetrix CEL analysis. Description:

P-MEXP-578

P-MEXP-579

P-MEXP-581

AtMYB60

Plants were grown in pots containing two parts of soil and one part of vermiculite, under long day condition (16hr light; 8 hr dark) at 22ºC, for 22 days.

Mature rosette leaves were frozen in liquid nitrogen and ground with 5ml of extraction buffer (100 mM Tris-HCl pH9, 1% SDS, 100 mM LiCl, 10 mM EDTA, 0.1% DEPC). The buffer was extracted twice with an equal volume of phenol-chloroform (1:1 v:v), and precipitated, overnight with 1 volume of 4 M LiCl, at 4°C. RNA was pelleted by centrifugation (30 min., 8000 rpm. 4°C), washed with 1ml of 70% Ethanol and resuspended in 500 ml of 0.1% DEPC H2O.

For the Arabidopsis spots, we first addressed within-slide normalization by plotting for each single slide a "MA plot" (Yang et al., 2002) where M = log2 (R/G) (with R = red fluorescent dye Cy5 and G = green fluorescent dye Cy3) and A = log2 (SQRT(RxG)) for each spot. To correct for dye intensity differences, we used the robust scatter plot smoother “LOWESS” as described by Yang et al. (2002) and implemented in Genstat (Payne and Arnold, 2003), to perform a local A-dependent normalization log2 (R/G) -> log2 (R/G) –c(A) =  log2(R/(c(A)G), where c(A)  is the lowess fit to the MA-plot. The user-defined smoothing parameter f, which is the fraction of the data used for smoothing at each point, was set at 20%. Based on the adjusted M and A values for each gene, adjusted log2R and log2G signal intensities were obtained.   Description of the quantitation types in the normalised datasets:   1. log2ratio = log2 ("AR VOL - RFU_cy5" / "AR VOL - RFU_cy3") ( M-value from M vs. A plot)  2. fit = result of the best lowess fit  3. log2mean = log2 (SQRT("AR VOL - RFU_cy5" * "AR VOL - RFU_cy3")) (Average intensity, A-value from M vs. A plot)  4. res = corrected log2ratio after the loess fit (residuals = log2ratio - fit)  5. newlog2R = log2 of corrected Cy5 intensity, calculated from residuals  6. newlog2G = log2 of corrected Cy3 intensity, calculated from residuals  7. newR = the corrected Cy5 intensity after loess fit  8. newG = the corrected Cy3 intensity after loess fit 

P-MTAB-4772

Starting at ~4 years of age, rhesus macaques were subjected to continuous 30% CR diet for ~8 years. Other rhesus macaques served as age- and body weight-matched controls (CON), and were fed approximately ad libitum. In both groups, food was provided daily at 8:00 h and 15:00 h, and consisted of specially formulated biscuits (Cargill, Minneapolis, MN, USA) supplemented with daily fresh fruits or vegetables (10 - 40 cal). The composition of the diet was 15% protein, 5% fat and 5% fiber with a caloric content of ~3.7 kcal/g. The biscuits included a vitamin/mineral mix that was 40% higher than the recommended allowance for rhesus macaques by the NRC, but were otherwise similar to those used in many laboratory studies of rhesus macaques.

Transcription profiling of pituitary gland and testis of rhesus macaques fed a normal or moderately calorie restricted diet

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