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Sample GSM1119747 Query DataSets for GSM1119747
Status Public on Jul 21, 2014
Title Aorta_High Fat-Sugar diet+Resveratrol_ Rep-6
Sample type RNA
 
Source name Thoracic aorta_High Fat-Sugar diet+Resveratrol_ Rep-6
Organism Macaca mulatta
Characteristics developmental stage: adult
gender: Male
diet: high fat/high sucrose (HFS) diet
agent: Resveratrol
tissue: Thoracic aorta
Treatment protocol After baseline assessment, the twenty four male rhesus monkeys were quasi- randomized into one of three groups: a high fat/high sucrose (HFS) diet (n=10); a HFS diet supplemented with resveratrol (HFS+R) (n=10); or, remaining on the healthy standard diet (SD) (n=4). The standard diet was a purified biscuit consisting of 13% of kcal in fat and less than 5% sucrose by weight. The HFS diet was a specially formulated purified ingredient diet with 42% of kcal in fat and approximately 27% sucrose by weight (Harlan, Teklad, Madison, WI). The monkeys were gradually switched to the HFS diet over a 3-week period. All groups received 2 meals per day of the specified diet in allotments that represent ad libitum feeding, yet consumption was isocaloric across groups.
Resveratrol was supplied by DSM Nutritional Products (Parsippany, NJ) and the dosing for monkeys was determined to be 40.7 mg. The resveratrol was used to formulate a flavored primate treat (Bi-Serv, Frenchtown, NJ) and given to the monkeys prior to each meal, thus, the monkeys received a total dose of 80 mg per day. All monkeys, regardless of weight, received the same amount of resveratrol. Monkeys in non-resveratrol groups receive a placebo treat. After completion of data collection at the one year time point, the resveratrol dose was increased to 240 mg per day.
After baseline assessment, 10 male rhesus monkeys were begun on a high fat/high sucrose (HFS) diet (n=10) plus Resveratrol; the HFS diet was a specially formulated purified ingredient diet with 42% of kcal in fat and approximately 27% sucrose by weight (Harlan, Teklad, Madison, WI). The monkeys were gradually switched to the HFS diet over a 3-week period. All groups received 2 meals per day of the specified diet in allotments that represent ad libitum feeding, yet consumption was isocaloric across groups. Resveratrol treatment for the first year was 80mg per day. At the one year time point they were switched to 240mg per day until the end of 2 years of dietary intervention.
Growth protocol Twenty-four adult (7-13 years old) male rhesus monkeys (Macaca mulatta) were housed individually in standard nonhuman primate caging on a 12h light/12h dark cycle, room temperature (78 +/- 2 degrees F), and humidity at 60 +/- 20%. One pairing was maintained throughout the study; all other monkeys had extensive visual, auditory, and olfactory but limited tactile contact with monkeys housed in the same room. Monkeys received 2 meals per day at estimated ad libitum levels throughout the study. Water was always available ad libitum. Monkeys were monitored minimally 3 times daily by trained animal care staff. During baseline assessments, all monkeys were maintained on a commercially available closed formula monkey chow (TestDiet #5038 Purina Mills, Richmond, IN).
Extracted molecule total RNA
Extraction protocol RNA was isolated from rhesus monkey aorta at 24-months of dietary intervention using Trizol reagent (Invitrogen) and further purified using RNeasy mini columns (Qiagen). Quality and Quantity were tested with an Agilent Bio-Analyzer using RNA 6000-Nano Chips.
Label biotin
Label protocol Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5ug of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.
 
Hybridization protocol Standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's SentrixHumanHT-12 v4 Expression BeadChips (Illumina, San Diego, CA). Each array on the HumanHT-12 v4 Expression BeadChip targets more than 47,000 probes derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq Release 38 (November 7, 2009) and other sources and offers genome-wide transcriptional coverage of well-characterized genes, gene candidates, and splice variants, with approximately 15-fold redundancy. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.
Scan protocol Arrays were scanned at a resolution of 0.8um using the Beadstation 500 X from Illumina.
Description Samplename: AR_96C029
Aorta_High Fat-Sugar diet+Resveratrol_ Rep-6
Data processing Data was extracted using the Illumina GenomeStudio software(v1.6.0). Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below. Z-score = (raw value - avg)/std.
 
Submission date Apr 09, 2013
Last update date Jun 22, 2020
Contact name Supriyo De
Organization name NIA-IRP, NIH
Department Laboratory of Genetics and Genomics
Lab Computational Biology & Genomics Core
Street address 251 Bayview Blvd
City Baltimore
State/province Maryland
ZIP/Postal code 21224
Country USA
 
Platform ID GPL10558
Series (1)
GSE45927 Resveratrol prevents diet-induced arterial degeneration and stiffening in nonhuman primates

Data table header descriptions
ID_REF
VALUE Z_VALUE (Z transformation of the natural log of the raw intensity values)
Detection Pval Detection Pvalue from Illumina GenomeStudio software, ver 1.6.0.

Data table
ID_REF VALUE Detection Pval
ILMN_1343291 7.52300984 0
ILMN_1343295 3.695430571 0
ILMN_1651199
ILMN_1651209
ILMN_1651210
ILMN_1651221 0.076289593 0.02857
ILMN_1651228 -0.506770489 0.6987
ILMN_1651229 0.990405307 0
ILMN_1651230
ILMN_1651232
ILMN_1651235
ILMN_1651236
ILMN_1651237
ILMN_1651238
ILMN_1651249
ILMN_1651253 -0.666007608 0.74416
ILMN_1651254 6.015623732 0
ILMN_1651259 -0.001953936 0.08571
ILMN_1651260
ILMN_1651262 3.012872223 0

Total number of rows: 47323

Table truncated, full table size 1063 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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