|
| Status |
Public on Apr 26, 2019 |
| Title |
Leg skin_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Leg skin, replicate 1
|
| Organism |
Gallus gallus |
| Characteristics |
tissue: Leg skin
developmental stage: 9 weeks
|
| Treatment protocol |
The dorsal skin was divided into two halves according to dorsal line axis. The right dorsal and leg skin were sampled, immediately frozen in liquid nitrogen, and stored at –80˚C.
|
| Growth protocol |
Skin samples used in the present study were collected from a chicken breeding line in Jiangsu Li-hua Animal Husbandry Company (Jiangsu, China). All chickens lived under the same conditions and were raised using a standardized feeding method with free access to water.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to The Agilent Chicken（V2）Gene Expression Microarray (4*44K) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.
|
| |
|
| Submission date |
Apr 25, 2019 |
| Last update date |
Apr 26, 2019 |
| Contact name |
gaige ji |
| E-mail(s) |
[email protected]
|
| Organization name |
Jiangsu Institute of Poultry Science
|
| Street address |
no.58, Cang jie Road
|
| City |
Yangzhou |
| ZIP/Postal code |
225125 |
| Country |
China |
| |
|
| Platform ID |
GPL15357 |
| Series (1) |
| GSE130293 |
Microarray analysis of molecular pathways and candidate genes between dorsal and leg Skin in Chicken |
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