|
| Status |
Public on Apr 18, 2012 |
| Title |
7-week-old chicken leg muscle (normal recessive White Rock chicken / dwarf recessive White Rock chicken), rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
dwarf chicken leg muscle
|
| Organism |
Gallus gallus |
| Characteristics |
breed: dwarf recessive White Rock
tissue: leg muscle
age: 7 weeks
identifier: B2b
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Animal Tissue RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada) following the manufacturer's recommended protocol.
|
| Label |
Cy3
|
| Label protocol |
The assay started from 2 to 5 ug total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore). The small RNAs (< 300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags (Cy3/Cy5) were used for the two RNA samples in dual-sample experiments.
|
| |
|
| Channel 2 |
| Source name |
normal chicken leg muscle
|
| Organism |
Gallus gallus |
| Characteristics |
breed: normal recessive White Rock
tissue: leg muscle
age: 7 weeks
identifier: A2b
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Animal Tissue RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada) following the manufacturer's recommended protocol.
|
| Label |
Cy5
|
| Label protocol |
The assay started from 2 to 5 ug total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore). The small RNAs (< 300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags (Cy3/Cy5) were used for the two RNA samples in dual-sample experiments.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).
|
| Scan protocol |
Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Devices) and digitized using Array-Pro image analysis software (Media Cybernetics).
|
| Description |
Meat-type chickens.
The body weight of dwarf chickens was about 30% less than that of normal chickens.
3 chickens used per breed for each sample.
|
| Data processing |
Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression). For two-color experiments, the ratio of the two sets of detected signals (log2 transformed, balanced) and p-values of the t-test were calculated; differentially detected signals were those with less than 0.01 p-values.
|
| |
|
| Submission date |
Apr 17, 2012 |
| Last update date |
Apr 18, 2012 |
| Contact name |
Hongmei Li |
| E-mail(s) |
lhm-lhm@sohu.com
|
| Phone |
13316044567
|
| Organization name |
south china agricultural university
|
| Street address |
Guangzhou tianhe wushan street
|
| City |
Guangzhou |
| ZIP/Postal code |
510640 |
| Country |
China |
| |
|
| Platform ID |
GPL15455 |
| Series (2) |
| GSE37367 |
Let-7b regulates skeletal muscle growth, development and fat deposition in deletion-type dwarf chickens (7-week-old chickens) |
| GSE37368 |
Let-7b regulates skeletal muscle growth, development and fat deposition in deletion-type dwarf chickens |
|
