Expression data from epididymal fat tissues of diet induced obese rats
From ArrayWiki
| PubMed ID: | none |
|---|---|
| Contact: | Dan Li
|
| Species: | Rattus norvegicus |
| Platform: | Affymetrix GeneChip Rat Genome 230 2.0 Array |
| Number of Samples: | 15 |
| Date Range: | 05/25/2006 - 05/25/2006 |
| Experiment Quality: | 98.98 0.79 % |
| Link to Repository: | GSE8700 |
| Original Intensity Data: | Download |
| Clean Intensity Data: | Download |
| Original PLIER Data: | Download |
| Clean PLIER Data: | Download |
| Clean CEL Files: | |
| Data Rank: | 
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Analysis of gene expression profiles of epididymal fat from DIO rats
We applied a comparative functional genomics approach to evaluate diet-induced obese (DIO) rats as an obesity model
Design: Gene expression profiles from DIO and lean rats were generated and compared. A private colony of male Long-Evans rats was set up at Harlan (Harlan-Sprague Dawley, Indianapolis, IN). The animals had been on either a high fat/high sucrose diet (TD95217, Harlan Takled, Madison, WI) or a regular chow (Purina 5008; Ralston-Purina, St. Louis, MO) since weaning. Rats were shipped at 14-weeks of age to our facility and maintained on a 12:12-hour light-dark photoperiod (light on 10:00 PM). They were individually housed throughout the study at ambient temperature, and had free access to diets and water. After 2 weeks acclimation to the facility, body weight of the rats and weight of food consumed in the last 7 days were measured once a week. Body fat mass was analyzed by nuclear magnetic resonance (NMR) using an Echo Medical System (Houston, TX) instrument 3 times throughout the study. Fat free mass is the difference between body mass and fat mass. All animal studies were conducted in compliance with approved institutional animal care and use protocols according to NIH guidelines (NIH publication No. 86-23, 1985). OGTT was conducted after an overnight fasting when animals were 21 weeks of age. After a baseline blood collection (time 0), animals were dosed orally with 1.5 gram/kg glucose. Subsequence blood samples were collected at 30, 60, and 120 minutes post glucose challenge for the determination of plasma glucose and insulin levels. At 25 weeks of age, blood was collected by tail bleeding after overnight fasting. Rats were killed a week later at 09:00am by rapid decapitation. Trunk blood was collected and epididymal fat tissue excised. Various circulating metabolic parameters were measured under fasted (week 25) and fed conditions (week 26). Total RNA from rat epididymal fat was isolated with RNA STAT-60 (Tel-Test) according to the manufacturer's protocol. 5 micrograms of total RNA were labeled and hybridized to Affymetrix RAE230_2 arrays according to the Affymetrix protocol.
Type: single time point, comparison control animal vs. diet induced obese animal
Contents |
[edit] Contributors
- Shuyu Li
- Yanyun Chen
[edit] Protocols
[edit] References
[edit] Links
GEO Accession for this experiment: GSE8700. (Public on Aug 07 2007)
RAW data: tar file.
[edit] Analysis
 Before Normalization |
 After Normalization & Cleaning |
[edit] Samples/Quality Control
| Sample | Date Scanned | Source Link | Probe Variance Data | Artifact Mask | Quality Score |
|---|---|---|---|---|---|
| Diet Induced Obese rat C1 | 05/25/2006 14:33:23 | GSM215572 | 
| 
| 99.2442 0.00 % |
| Diet Induced Obese rat C2 | 05/25/2006 17:21:27 | GSM215573 | 
| 
| 99.1393 0.30 % |
| Diet Induced Obese rat C3 | 05/25/2006 17:28:55 | GSM215574 | 
| 
| 98.1948 9.17 % |
| Diet Induced Obese rat C5 | 05/25/2006 16:51:30 | GSM215575 | 
| 
| 99.1098 0.04 % |
| Diet Induced Obese rat C6 | 05/25/2006 16:58:52 | GSM215576 | 
| 
| 98.4128 0.27 % |
| Diet Induced Obese rat C7 | 05/25/2006 17:13:40 | GSM215577 | 
| 
| 99.0613 0.19 % |
| Diet Induced Obese rat C8 | 05/25/2006 17:06:14 | GSM215578 | 
| 
| 99.1185 0.18 % |
| control lean rat A1 | 05/25/2006 15:29:15 | GSM215579 | 
| 
| 99.1083 0.42 % |
| control lean rat A2 | 05/25/2006 15:21:51 | GSM215580 | 
| 
| 99.0357 0.03 % |
| control lean rat A3 | 05/25/2006 15:14:23 | GSM215581 | 
| 
| 99.0405 0.08 % |
| control lean rat A4 | 05/25/2006 15:07:02 | GSM215582 | 
| 
| 98.9836 0.06 % |
| control lean rat A5 | 05/25/2006 14:59:39 | GSM215583 | 
| 
| 99.1584 0.39 % |
| control lean rat A6 | 05/25/2006 14:52:11 | GSM215584 | 
| 
| 99.0358 0.52 % |
| control lean rat A7 | 05/25/2006 14:08:45 | GSM215585 | 
| 
| 99.0643 0.00 % |
| control lean rat A8 | 05/25/2006 16:36:43 | GSM215586 | 
| 
| 99.0111 0.24 % |
