|
| Status |
Public on May 09, 2016 |
| Title |
Heat-conditioned-21°C C4 vs. Control-21°C T4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Pectoralis major muscle
|
| Organism |
Gallus gallus |
| Characteristics |
strain: Cobb 500
gender: male
age: 34 days posthatch
incubation treatment: Heat-conditioned
ambient temperature at 34 days (°c): 21
|
| Treatment protocol |
Eggs were either incubated in standard conditions (Controls T, 37.8°C and 56% relative humidity RH during all embryogenesis) or submitted to heat during incubation (heat-conditioned C, 39.5°C and 65% RH during 12h/d from day 7 to 16 of embryogenesis). At 34 days posthatch they were submitted to a heat challenge (32°C during 5h, respectively TCH and CCH) or not (21°C, respectively T and C). Chickens were characterized by low body temperatures in C and CCH treatments and high body temperatures in T and TCH treatments.
|
| Growth protocol |
Cobb500 eggs were incubated at INRA UE1295 PEAT before chickens were reared in standard conditions until 34d of age
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from Pectoralis major muscle using the Qiagen RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) and Cyanine-5 (Cy5) labeled cRNAs were prepared from 100 ng of total RNA using the Two-Color Low Input Quick Amp Labeling Kit (Agilent Technologies). Synthetic RNAs (Two-Color RNA Spike-In Kit, Agilent Technologies) were added as an internal quality control. The obtained cRNAs were purified using RNeasy Mini Spin columns (Qiagen) and subsequently run onto a Bioanalyzer 2100 using RNA 6000 Nano chips (Agilent Technologies) to assess their profiles.
|
| |
|
| Channel 2 |
| Source name |
Pectoralis major muscle
|
| Organism |
Gallus gallus |
| Characteristics |
strain: Cobb 500
gender: male
age: 34 days posthatch
incubation treatment: Control
ambient temperature at 34 days: 21
|
| Treatment protocol |
Eggs were either incubated in standard conditions (Controls T, 37.8°C and 56% relative humidity RH during all embryogenesis) or submitted to heat during incubation (heat-conditioned C, 39.5°C and 65% RH during 12h/d from day 7 to 16 of embryogenesis). At 34 days posthatch they were submitted to a heat challenge (32°C during 5h, respectively TCH and CCH) or not (21°C, respectively T and C). Chickens were characterized by low body temperatures in C and CCH treatments and high body temperatures in T and TCH treatments.
|
| Growth protocol |
Cobb500 eggs were incubated at INRA UE1295 PEAT before chickens were reared in standard conditions until 34d of age
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from Pectoralis major muscle using the Qiagen RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions.
|
| Label |
Cy5
|
| Label protocol |
Cyanine-3 (Cy3) and Cyanine-5 (Cy5) labeled cRNAs were prepared from 100 ng of total RNA using the Two-Color Low Input Quick Amp Labeling Kit (Agilent Technologies). Synthetic RNAs (Two-Color RNA Spike-In Kit, Agilent Technologies) were added as an internal quality control. The obtained cRNAs were purified using RNeasy Mini Spin columns (Qiagen) and subsequently run onto a Bioanalyzer 2100 using RNA 6000 Nano chips (Agilent Technologies) to assess their profiles.
|
| |
|
| |
| Hybridization protocol |
Transcriptome profiling was performed using a Custom Gene Expression 8x60K Gallus gallus array (Agilent Technologies). A total of 64 samples were analyzed, corresponding to 8 slides. 300 ng of Cy3-labeled cRNA (specific activity >9) and 300 ng of Cy5-labeled cRNA (specific activity >9) were combined for each single array, and the washing steps were then performed according to the manufacturer’s recommendations.
|
| Scan protocol |
The slides were scanned using a G2565CA Scanner System (Agilent Technologies), using a scan protocol with a resolution of 3 µm and a dynamic range of 20 bit.
The resulting .tiff images were analyzed with Feature Extraction Software (Agilent Technologies) using the GE2_107_Sep09 protocol to obtain background subtracted and spatially detrended Processed Signal intensities.
|
| Data processing |
The data were filtered on the basis of information on the quality of the spots for the normalization step considering that the signal must be more than 1.5 times the background noise. Normalization was performed by global loess function of the package Limma (Smyth, 2004).
|
| |
|
| Submission date |
Jul 10, 2015 |
| Last update date |
May 09, 2016 |
| Contact name |
Anne Collin |
| E-mail(s) |
Anne.Collin@tours.inra.fr
|
| Organization name |
INRA
|
| Lab |
URA
|
| Street address |
UR83 Recherches Avicoles
|
| City |
Nouzilly |
| ZIP/Postal code |
F-37380 |
| Country |
France |
| |
|
| Platform ID |
GPL20679 |
| Series (1) |
| GSE70756 |
Embryo thermal manipulation: muscle transcriptional profile in chickens submitted or not to heat challenge 34d posthach |
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