|
| Status |
Public on Sep 13, 2011 |
| Title |
epiWAT LGI replicate 09 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
epididymal white adipose tissue, high fat, low glycemic index diet (LGI)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
gender: male
developmental stage: adult
tissue: epididymal white adipose tissue
|
| Treatment protocol |
Animals were fed a purified high fat (30 energy% fat) diet, as published (Faseb J 2009; 23:1092-1101). The carbohydrate fraction of the high fat diets had either a low glycemic index (LGI) or a high glycemic index (HGI), which were fed to two groups of mice for 13 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from epididymal WAT as described (Faseb J 2009; 23:1092-1101), quantified using Nanodrop and qualified using Experion Automated Electrophoresis System.
|
| Label |
Cy5
|
| Label protocol |
500 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol version 3.1 , as described previously (Am J Clin Nutr 2008; 87:181-189).
|
| |
|
| Channel 2 |
| Source name |
epididymal white adipose tissue, reference pool of all LGI and HGI samples
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
gender: male
developmental stage: adult
tissue: epididymal white adipose tissue
|
| Treatment protocol |
Animals were fed a purified high fat (30 energy% fat) diet, as published (Faseb J 2009; 23:1092-1101). The carbohydrate fraction of the high fat diets had either a low glycemic index (LGI) or a high glycemic index (HGI), which were fed to two groups of mice for 13 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from epididymal WAT as described (Faseb J 2009; 23:1092-1101), quantified using Nanodrop and qualified using Experion Automated Electrophoresis System.
|
| Label |
Cy3
|
| Label protocol |
500 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol version 3.1 , as described previously (Am J Clin Nutr 2008; 87:181-189).
|
| |
|
| |
| Hybridization protocol |
Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent In Situ Hybridization Kit Plus. Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized at 65C for 17 hours at 4rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations using a Cy5-dyesaver as published (Anal Biochem 2007_363_315).
|
| Scan protocol |
Scanned on an Agilent G2505C scanner.
|
| Description |
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
|
| Data processing |
Images were quantified using Agilent Feature Extraction Software (v 9.5.1.1) to obtain raw median signal and background values for both Cy5 and Cy3. Spots with a mean signal higher than twice the background value over all arrays were considered to be expressed. Data was normalized according to Pellis et al., (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, LOWESS normalization, and log2 transformation.
|
| |
|
| Submission date |
Jan 28, 2011 |
| Last update date |
Sep 14, 2011 |
| Contact name |
Evert M. van Schothorst |
| E-mail(s) |
evert.vanschothorst@wur.nl
|
| Organization name |
Wageningen University
|
| Lab |
Human and Animal Physiology
|
| Street address |
De Elst 1
|
| City |
Wageningen |
| ZIP/Postal code |
6708 WD |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL7042 |
| Series (1) |
| GSE26930 |
Glycemic index differences of high-fat diets modulate primarily lipid metabolism in murine adipose tissue |
|
