|
| Status |
Public on Feb 03, 2015 |
| Title |
[S660-187 EW-LPN Cy3]-[S572-187 EW-MPN Cy5] |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Longissimus dorsi
|
| Organism |
Bos taurus |
| Characteristics |
breed: Angus × Simmental
tissue: Skeletal muscle
weaning: Early weaning
maternal plane of nutrition: Low Plane Nutrition
age (days): 187
|
| Treatment protocol |
Aberdeen Angus × Simmental steers used in this study came from cow that received a low and a high plane of nutrition during the last 90 days before calving. Offsprings from these cows were selected to be early or normal weaned.
|
| Growth protocol |
Aberdeen Angus × Simmental steers were early or normal weaned.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A sample of Longissimus dorsi muscle was disected and snap-frozen in liquid nitrogen. Tissue was weighted (~0.5 g) and RNA extracted using ice-cold TRIZol. Genomic DNA was removed from RNA with DNAse (Qiagen) using RNeasy Mini Kit columns (Qiagen)
|
| Label |
Cy3
|
| Label protocol |
Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript III Kit (Invitrogen) as manufacturers instructions.
|
| |
|
| Channel 2 |
| Source name |
Longissimus dorsi
|
| Organism |
Bos taurus |
| Characteristics |
breed: Angus × Simmental
skeletal muscle tissue: Skeletal muscle
weaning: Early weaning
maternal plane of nutrition: Medium Plane Nutrition
age (days): 187
|
| Treatment protocol |
Aberdeen Angus × Simmental steers used in this study came from cow that received a low and a high plane of nutrition during the last 90 days before calving. Offsprings from these cows were selected to be early or normal weaned.
|
| Growth protocol |
Aberdeen Angus × Simmental steers were early or normal weaned.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A sample of Longissimus dorsi muscle was disected and snap-frozen in liquid nitrogen. Tissue was weighted (~0.5 g) and RNA extracted using ice-cold TRIZol. Genomic DNA was removed from RNA with DNAse (Qiagen) using RNeasy Mini Kit columns (Qiagen)
|
| Label |
Cy5
|
| Label protocol |
Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript III Kit (Invitrogen) as manufacturers instructions.
|
| |
|
| |
| Hybridization protocol |
Labelled cDNA hybridised using 80 μL of the hybridization buffer #1 (Ambion). Slides placed in humidified slide chambers (Corning) in water bath for 40 h at 42 °C. Prior scanning the microarray were washed for 5 min by agitation 3 times with wash buffers in the following order: 1×SSC and 0.2% SDS solution preheated at 42°C, 0.1×SSC and 0.2% SDS solution, and 0.1×SSC solution. Lastly, slides were inserted into a 50 mL tube, spin-dried and gassed with Argon to preserve dye from bleaching.
|
| Scan protocol |
Arrays were scanned with a ScanArray 4000 (GSI-Lumonics) dual-laser confocal scanner and images were processed and edited using GenePix 6.0 (Axon Instruments).
|
| Description |
Sample were total RNA from bovine skeletal muscle tissue (Longissimus dorsi)
|
| Data processing |
Array quality was assessed using an in-house parser written in Perl language. Spots that received a -100 flag by GenePix 6.0 were removed from further analysis and background intensity was subtracted from the foreground intensity. Spots on the slide were considered “good” if the median intensity was ≥3 standard deviation above median background for each channel (i.e., dye). Spots were flagged “present” when both dyes passed the criteria, “marginal” if only one dye passed the criteria, or “absent” when both dyes failed to pass the criteria. Statistical analysis was conducted on oligos that were flagged as “present” and “marginal”. Data from a total of 30 microarrays were normalized for dye and array effects (i.e., Loess normalization and array centering and scaling) before statistical analysis.
|
| |
|
| Submission date |
Feb 03, 2015 |
| Last update date |
Feb 03, 2015 |
| Contact name |
Sonia Josefina Moisá |
| Organization name |
University of Illinois
|
| Department |
Animal Sciences
|
| Lab |
Nutriphysiogenomics
|
| Street address |
1207 W. Gregory Dr.
|
| City |
Urbana |
| State/province |
IL |
| ZIP/Postal code |
61801 |
| Country |
USA |
| |
|
| Platform ID |
GPL11649 |
| Series (1) |
| GSE65560 |
Maternal Plane Of Nutrition During Late Gestation And Weaning Age Alter Offspring Transcriptome Profiles Of Longissimus Muscle In Angus × Simmental |
|
