|
| Status |
Public on Sep 08, 2015 |
| Title |
Patient 6 S12 |
| Sample type |
RNA |
| |
|
| Source name |
normal liver tissue
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: Non-alcoholic fatty liver disease (NAFLD)
patient id: Patient 6
gender: male
age: 40 years
tissue: normal liver tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.
|
| Label |
Cy3
|
| Label protocol |
Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.
|
| |
|
| Hybridization protocol |
1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.
|
| Scan protocol |
The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C)
|
| Description |
S12.txt
|
| Data processing |
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.
|
| |
|
| Submission date |
Sep 07, 2015 |
| Last update date |
Sep 08, 2015 |
| Contact name |
sun chuanzheng |
| E-mail(s) |
zheng-1016@hotmail.com
|
| Phone |
13574841516
|
| Organization name |
The Third Xiangya Hospital of Central South Uiversity
|
| Street address |
tongzhipo
|
| City |
Changsha |
| ZIP/Postal code |
410013 |
| Country |
China |
| |
|
| Platform ID |
GPL16956 |
| Series (1) |
| GSE72756 |
Genome-wide analysis of long noncoding RNA expression profile in non-alcoholic fatty liver disease |
|
