|
| Status |
Public on Jun 01, 2011 |
| Title |
bcmo1 ko male under BC diet 3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
inguinal adipose tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57/BL6;129Svj background
gender: male
genotype/variation: bcmo1 knockout
diet: BC
diet intervention started: 5 weeks old
age at sacrifice: 19 weeks old
tissue: inguinal adipose tissue
|
| Treatment protocol |
five-week-old WT and BCMO1 KO male and female mice were fed a defined, pelletized diet containing 1500 IU vitamin A/kg and 10% energy as fat, without or with 150 mg BC/kg diet for 14 weeks prior euthanasia.
|
| Growth protocol |
Mice experiment was conducted according to accepted standard and humane care and use of laboratory animals, and was approved by the bioethical committee of the University of Freiburg (Germany). During the weaning period up to 5 weeks of age all mice were maintained on breeder chow containing 14000 IU of vitamin A/kg diet (Provima kliva AG, Switzerland).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
On the day of euthanization, blood was taken from the vena cava under unesthesia. The animals were then killed and tissues (including inguinal adipose tissue) were dissected.
|
| Label |
cy5
|
| Label protocol |
cDNA was synthesized from 1 µg of inguinal adipose tissue total RNA using the Agilent Low RNA Input Fluorescent Linear Amplification Kit for each animal without addition of spikes. Thereafter samples were split in 2 equal amounts, to synthesize Cyanine 3-CTP (Cy3) and Cyanine 5-CTP (Cy5) labeled cRNA using half the amounts as indicated by the manufacturer per dye (Agilent Technologies). Labelled cRNA was purified using RNeasy columns (Qiagen). 1200 ng of every Cy3 labeled cRNA sample was pooled and used as a common reference pool.
|
| |
|
| Channel 2 |
| Source name |
inguinal adipose tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57/BL6;129Svj background
tissue: inguinal adipose tissue
sample type: common reference pool (representing every Cy3 labeled cRNA sample)
|
| Treatment protocol |
five-week-old WT and BCMO1 KO male and female mice were fed a defined, pelletized diet containing 1500 IU vitamin A/kg and 10% energy as fat, without or with 150 mg BC/kg diet for 14 weeks prior euthanasia.
|
| Growth protocol |
Mice experiment was conducted according to accepted standard and humane care and use of laboratory animals, and was approved by the bioethical committee of the University of Freiburg (Germany). During the weaning period up to 5 weeks of age all mice were maintained on breeder chow containing 14000 IU of vitamin A/kg diet (Provima kliva AG, Switzerland).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
On the day of euthanization, blood was taken from the vena cava under unesthesia. The animals were then killed and tissues (including inguinal adipose tissue) were dissected.
|
| Label |
cy3
|
| Label protocol |
cDNA was synthesized from 1 µg of inguinal adipose tissue total RNA using the Agilent Low RNA Input Fluorescent Linear Amplification Kit for each animal without addition of spikes. Thereafter samples were split in 2 equal amounts, to synthesize Cyanine 3-CTP (Cy3) and Cyanine 5-CTP (Cy5) labeled cRNA using half the amounts as indicated by the manufacturer per dye (Agilent Technologies). Labelled cRNA was purified using RNeasy columns (Qiagen). 1200 ng of every Cy3 labeled cRNA sample was pooled and used as a common reference pool.
|
| |
|
| |
| Hybridization protocol |
Individual 825 ng Cy5-labeled cRNA and 825 ng pooled Cy3-labeled cRNA were fragmentated in 1x fragmentation and 1x blocking agent (Agilent Technologies) at 60 °C for 30 minutes and thereafter mixed with Gex Hybridization Buffer HI-RPM (Agilent Technologies) and hybridized in a 1:1 ratio at 65 °C for 17 h in an Agilent Microarray hybridization chamber rotating at 4 rpm. After hybridization slides were washed according to the wash protocol with Stabilization and Drying solution (Agilent Technologies).
|
| Scan protocol |
Arrays were scanned at an Agilent scanner (G2505B) with 10% and 100% laser power intensities.
|
| Description |
biological replicate 3 of 6. BCMO1 KO male under BC diet
|
| Data processing |
Signal intensities for each spot were quantifed using feature extraction 9.1 (Agilent Technologies). Quality control for every microarray was performed visually by using ‘Quality’ control graphs from ‘Feature’extraction and M-A plots and boxplots, which were made using limmaGUI in R (Bioconductor).
|
| |
|
| Submission date |
Feb 13, 2011 |
| Last update date |
Jun 01, 2011 |
| Contact name |
Jaume Amengual |
| E-mail(s) |
[email protected]
|
| Phone |
+216 368 0970
|
| Organization name |
case western reserve university
|
| Department |
Pharmacology
|
| Street address |
2109 Aderbert Rd
|
| City |
Cleveland |
| State/province |
Ohio |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL4134 |
| Series (2) |
| GSE27271 |
Adipose tissue analysis of wild-type and beta-carotene 15-15'-oxygenase 1 (Bcmo1) ko mice fed under control diet and beta-carotene diet |
| GSE98847 |
Nutritional effects by beta-carotene versus control in lung, inguinal white adipose tissue, and liver in males and females of control wildtype mice versus BCMO/BCO1 knockout mice |
|
