|
| Status |
Public on Jun 06, 2016 |
| Title |
Rumenpapillae_high-concentrate_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Rumen papillae, high-concentrate,cow 3
|
| Organism |
Bos taurus |
| Characteristics |
breed: Holstein cattle
gender: female
diet: high-concentrate diet (HC; 70% concentrate feed)
tissue: Rumen papillae
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIZOL Reagent according to manufacturer's instruction (Life Technologies, Carlsbad, CA, US). The RNA quantity and purity were determined by NanoDrop ND-1000 spectrophotometer at 260/280 nm. The integrity of total RNA was assessed with an Agilent Bioanalyzer 2100. The RNA Integrity Numbers (RINs) for the samples were obtained. All the RNA samples showed 7.6 or higher RIN values and 28S/18S > 1.5, indicating sufficient quality to be used for microarray.
|
| Label |
Cy3
|
| Label protocol |
Add 10 to 200 ng of total RNA to a 1.5-mL microcentrifuge tube in a final volume of 1.5 µL.Add 2 µL of diluted Spike Mix to each tube. Prepare and add T7 Promoter Primer.Prewarm the 5X first strand buffer at 80°C for 3 to 4 minutes to ensure adequate resuspensions of the buffer components.Prepare and add cDNA Master Mix.Prepare and add Transcription Master Mix.
|
| |
|
| Hybridization protocol |
Purify the labeled/amplified RNA.Prepare the 10X Blocking Agent.Prepare hybridization samples.Prepare the hybridization assembly.Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C.Hybridize at 65°C for 17 hours.Add Triton X-102 to Gene Expression wash buffers.Prewarm Gene Expression Wash Buffer 2.Always use clean equipment when doing the hybridization and wash steps.Arrays were incubated at 65C for 17h in Agilent microarray hybridization chambers and subsequently washed in staining dishes (Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Agilent technologies, Santa Clara, CA, US) and Stabilization and Drying Solution (Agilent Technologies, Santa Clara, CA, US) followed the manufacturer’s instructions.
|
| Scan protocol |
Slides were scanned by Agilent Microarray Scanner (Agilent Technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, US) with default settings
|
| Description |
H3-P1
|
| Data processing |
the 75th percentile signal value to normalize Agilent one-color microarray signals for inter-array comparisons.the data were processed refer to the Agilent G2567AA Feature Extraction Software Reference Guide.
|
| |
|
| Submission date |
Jun 05, 2016 |
| Last update date |
Jun 06, 2016 |
| Contact name |
ruiyang zhang |
| E-mail(s) |
zhangruiyangnjau@163.com
|
| Organization name |
nanjing agricultural university
|
| Department |
College of Animal Science and Technology
|
| Lab |
Laboratory of Gastrointestinal Microbiology
|
| Street address |
tongwei road weigang no. 1
|
| City |
Nanjing |
| State/province |
jiangsu |
| ZIP/Postal code |
210095 |
| Country |
China |
| |
|
| Platform ID |
GPL9712 |
| Series (1) |
| GSE82272 |
High-concentrate feeding upregulates the expression of inflammation-related genes in the ruminal epithelium of dairy cattle |
|
