|
| Status |
Public on Mar 15, 2018 |
| Title |
Liver_RegularDiet_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Liver tissue, mice fed regular food, replicate 2
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
diet: 100% granulated regular food
|
| Treatment protocol |
Approximately 0,5 g of liver tissue was collected from the right hepatic lobe, taking care to spare the neighboring major blood vessels. All liver samples were immediately immersed in RNAlater (Qiagen) and stored at -80 °C until further use
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA containing miRNA was extracted with TriReagent (Sigma-Aldrich), purified with RNeasy Mini Kit (Qiagen) and assessed for quality with Agilent 2100 Bioanalyzer (Agilent Technologies). All samples had the RNA Integrity Number (RIN) greater than 8.
|
| Label |
Cy3
|
| Label protocol |
The cRNA-Cy3 microarray probes were synthesized from 100 ng of total RNA using Agilent Low Input Quick Amp Labeling Kit. The quality of synthesized cRNAs was checked with Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies) considering a minimal yield of 1.65 μg and a specific activity of more than 6 pmol/μl Cy3/μg cRNA.
|
| |
|
| Hybridization protocol |
The probes were hybridized on Agilent G3 Mouse Gene Expression v.2 arrays. Hybridization was carried out for 17 hours at 65°C, then slides were washed and dried acording to the manufacturer's protocol. In addition, to avoid the ozone effects on Cy-3 signal, a supplementary organic solvent containing an ozone scavenging compound dissolved in acetonitrile was used after washing step.
|
| Scan protocol |
Slides were scanned on Agilent G2505C Microarray Scanner at 3 µm resolution.
|
| Data processing |
Microarray images were processed with Agilent Feature Extraction (FE) software v. 11.5.1.1, using protocol GE1_1105_Oct12 and design 074809_D_F_20150624. Data processing was done in R/Bioconductor using as input the raw median signals generated by FE. Data were filtered by removing control and flagged (saturated, non-uniform) featues, background corrected (method=normexp, offset=50) and quantile normalized between arrays. The intensities were summarized at the transcript level.
|
| |
|
| Submission date |
Mar 14, 2018 |
| Last update date |
Mar 15, 2018 |
| Contact name |
Ovidiu Balacescu |
| E-mail(s) |
[email protected]
|
| Phone |
0040 264 590 638
|
| Organization name |
The Oncology Institute “Prof Dr. Ion Chiricuta”,
|
| Department |
Functional Genomics, Proteomics and Experimental Pathology
|
| Street address |
34-36 Republicii
|
| City |
Cluj-Napoca |
| State/province |
Cluj |
| ZIP/Postal code |
400015 |
| Country |
Romania |
| |
|
| Platform ID |
GPL21810 |
| Series (1) |
| GSE111804 |
MicroRNAs mediate liver transcriptome changes upon soy diet intervention in mice |
|
