|
| Status |
Public on Jun 13, 2017 |
| Title |
Liver_Leghorn_wild-type_8670 |
| Sample type |
RNA |
| |
|
| Source name |
Liver_Leghorn_wild-type
|
| Organism |
Gallus gallus |
| Characteristics |
background breed: heterozygote cock 'Dw/dw' and normal Leghorn female
genotype/variation: wild type; normal (Dw/-)
Sex: female
tissue: liver
|
| Growth protocol |
No specific protocol for growth
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The liver was sampled from 24 dwarf and 24 normal-sized hens fed ad libitum and immediately frozen in liquid nitrogen. Total RNAs were extracted from approximately 100 mg of tissue using the RNeasy Midi Kit (Qiagen) according to the manufacturer's instructions. The RNAs were quantified by spectrophotometry using a NanoDrop ND-1000 (Thermo Fischer) and their quality was verified using an Bioanalyzer 2100 (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 labeled cRNAs were prepared from 100 ng of total RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). Subsequently, cRNA yields and specific activities were checked on a NanoDrop ND-1000 spectrophotometer (Thermo Scientific).
|
| |
|
| Hybridization protocol |
600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) were fragmented at 60 °C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent Fragmentation Buffer and 10x Agilent Blocking Agent and following the manufacturer's instructions. On completion of the fragmentation reaction, for each sample 25 µl of 2x Agilent Hybridization Buffer were added to the fragmentation mix and hybridized to a chicken Agilent Custom 8X60K Gene Expression Microarray (AMADID: 037360) for 17 hours at 65°C in a rotating Agilent Hybridization Oven. After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and for 1 minute at 37 °C with GE Wash buffer 2 (Agilent Technologies), then dried immediately.
|
| Scan protocol |
Slides were scanned immediately after washing using a G2565CA Scanner System (Agilent Technologies) using one color scan settings for 8X60K slides (scan area 61x21.6 mm).
|
| Data processing |
The scanned images were analyzed with the Feature Extraction Software v10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09 and Grid: 037360_D_F_20111109).
|
| |
|
| Submission date |
Dec 09, 2016 |
| Last update date |
Jun 13, 2017 |
| Contact name |
Tatiana Zerjal |
| E-mail(s) |
tatiana.zerjal@inra.fr
|
| Organization name |
INRA
|
| Department |
Animal Genetics
|
| Lab |
GABI
|
| Street address |
bat 211
|
| City |
Jouy en Josas |
| ZIP/Postal code |
78350 |
| Country |
France |
| |
|
| Platform ID |
GPL20588 |
| Series (1) |
| GSE91084 |
Transcriptomic analysis of liver in sex-linked Dwarf and wild type chickens |
|
