|
| Status |
Public on May 06, 2008 |
| Title |
Chicken Liver fed 4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Fed-4
|
| Organism |
Gallus gallus |
| Characteristics |
Male broiler chicks fed ad libitum Age: 4 weeks Tissue: Liver
|
| Growth protocol |
Standard broiler chicken growth protocol. Livers were rapidly excised, frozen in liquid nitrogen and stored at –75 °C until RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA)
|
| Label |
Cy5
|
| Label protocol |
Five µg of each mRNA sample were reverse-transcribed and Cy5 fluorescent-labelled using the ChipShot™ Direct Labeling kit (Promega, Charbonnieres, France).
|
| |
|
| Channel 2 |
| Source name |
Reference
|
| Organism |
Gallus gallus |
| Characteristics |
Male broiler chicks Age: 4 weeks Tissue: Liver
|
| Growth protocol |
Standard broiler chicken growth protocol. Livers were rapidly excised, frozen in liquid nitrogen and stored at –75 °C until RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA)
|
| Label |
Cy3
|
| Label protocol |
Five µg of each mRNA sample were reverse-transcribed and Cy3 fluorescent-labelled using the ChipShot™ Direct Labeling kit (Promega, Charbonnieres, France).
|
| |
|
| |
| Hybridization protocol |
The microarray was hybridized overnight at 42°C with Cy5-labeled Fed-2 cDNA and an aliquot of the Cy3-labeled reference cDNA using automatic hybridization chamber (Discovery from Ventana Medical System, Inc). Slides were washed in increasing stringency using salt sodium citrate.
|
| Scan protocol |
The microarray slides were scanned using a laser scanner (GenePix 4000A from Axon Instrument, CA) at 550 nM for Cy3 and 640 nM for Cy5 to generate two TIFF images for each slide.
|
| Description |
Feeding- fasting transition study in chicken liver
|
| Data processing |
The two images from each slide were analyzed with GenepixPro 4.0 software (Axon instruments, Inc., Union City, CA). Pre-processing and normalization of data were accomplished using the R-project statistical and Bioconductor environment (http://www.r-project.org) (http://www.bioconductor.org). For the normalization step, data were filtered according to 3 criterions based on 1) the genepix flag automatically performed by GenepixPro 4.0; 2) the SNR 3) the asymmetry spot (see Desert et Al 2008). The ratio Cy5/Cy3 used was expressed as the Log(base 2) of the ratio of median pixel intensity of the two red and green spots. Log2 median ratio values were then normalized using global LOWESS normalization.
|
| |
|
| Submission date |
Apr 29, 2008 |
| Last update date |
May 05, 2008 |
| Contact name |
Sandrine Lagarrigue |
| E-mail(s) |
sandrine.lagarrigue@agrocampus-rennes.fr
|
| Phone |
33 02 23 48 59 59
|
| Fax |
33 02 23 48 54 70
|
| Organization name |
Agrocampus Rennes/ INRA
|
| Lab |
UMR Genetique animale
|
| Street address |
65 rue de St Brieuc
|
| City |
Rennes |
| ZIP/Postal code |
35042 |
| Country |
France |
| |
|
| Platform ID |
GPL5480 |
| Series (1) |
| GSE11290 |
Transcriptome profiling of feeding-to-fasting transition in chicken liver using a chicken 20K oligo microarray |
|
