|
| Status |
Public on Sep 16, 2020 |
| Title |
Hereford semitendinosus muscle_Cy3 vs Holstein-Friesian semitendinosus muscle_Cy5_3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Hereford muscle_Cy3
|
| Organism |
Bos taurus |
| Characteristics |
breed: Hereford
age: 15 month old
tissue: m. semitendinosus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by using a total RNA kit (A&A BIOTECHNOLOGY, Poland). RNA quantity was measured spectrophotometrically using NanoDrop (NanoDrop Technologies, USA). The analysis of final RNA quality and integrity was performed with BioAnalyzer 2100 (Agilent Technologies, USA). To ensure optimal data quality only RNA samples with RIN number ≥ 9 were included into the analysis.
|
| Label |
Cy3
|
| Label protocol |
Low Input Quick Amp Labeling Kit (Agilent Technologies, USA) was used to amplify and label target RNA to generate complementary RNA (cRNA).
|
| |
|
| Channel 2 |
| Source name |
Holstein-Friesian muscle_Cy5
|
| Organism |
Bos taurus |
| Characteristics |
brred: Holstein-Friesian
age: 15 month old
tissue: m. semitendinosus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by using a total RNA kit (A&A BIOTECHNOLOGY, Poland). RNA quantity was measured spectrophotometrically using NanoDrop (NanoDrop Technologies, USA). The analysis of final RNA quality and integrity was performed with BioAnalyzer 2100 (Agilent Technologies, USA). To ensure optimal data quality only RNA samples with RIN number ≥ 9 were included into the analysis.
|
| Label |
Cy5
|
| Label protocol |
Low Input Quick Amp Labeling Kit (Agilent Technologies, USA) was used to amplify and label target RNA to generate complementary RNA (cRNA).
|
| |
|
| |
| Hybridization protocol |
Probe were hybridized using Gene Expression Hybridization Kit (Agilent Technologies, USA) according to the manufacturers protocol. RNA Spike In Kit (Agilent Technologies, USA) was used as an internal control.
|
| Scan protocol |
Acquisition and analysis of hybridization intensities were performed using the Agilent DNA microarray scanner and Agilent Feature Extraction software 10.7.3.1. according to the standard manufacturer’s procedures and LOWESS normalization.
|
| Description |
Biological replicate 3 of 4. Hereford semitendinosus muscle_Cy3 vs Holstein-Friesian semitendinosus muscle_Cy5_DYE SWAPPED to make Holstein-Friesian a reference sample_rep 3
|
| Data processing |
Linear Lowess normalized. The statistical analysis was performed using Gene Spring 13 software default protocol (Agilent Technologies, USA). The statistical significance of the differences was evaluated using student test (p<0.05) and fold change FC>1.3.
|
| |
|
| Submission date |
Sep 17, 2019 |
| Last update date |
Sep 16, 2020 |
| Contact name |
Tomasz Sadkowski |
| E-mail(s) |
tomasz_sadkowski@sggw.pl
|
| Phone |
+48225936263
|
| Fax |
+48228472452
|
| URL |
http://sadkowski.info
|
| Organization name |
Warsaw University of Life Sciences - SGGW
|
| Department |
Department of Physiological Sciences
|
| Street address |
Nowoursynowska 159
|
| City |
Warsaw |
| ZIP/Postal code |
02-776 |
| Country |
Poland |
| |
|
| Platform ID |
GPL11648 |
| Series (1) |
| GSE137565 |
Transcriptomic profile of semitendinosus muscle of bulls of different breed and performance (Hereford vs Holstein-Friesian) |
|
