|
| Status |
Public on Jan 13, 2017 |
| Title |
AML 6 |
| Sample type |
RNA |
| |
|
| Source name |
AML
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: bone marrow
cell type: mononuclear
disease state: AML
|
| Treatment protocol |
Mononuclear cells were extracted from patient bone marrows using FICOLL solution.
|
| Growth protocol |
RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from bone marrow mononuclear cells were extracted using TRIzol reagent following the manufacturer's instructions. ArrayStar lncRNA array V3 was performed to detect the differentially expressed lncRNAs and mRNAs.
|
| 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.
|
| |
|
| Hybridization protocol |
The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.
|
| Scan protocol |
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.
|
| Description |
Total RNA from bone marrow mononuclear cells were extracted using TRIzol reagent following the manufacturer's instructions
|
| Data processing |
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 6 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 |
Aug 01, 2016 |
| Last update date |
Jan 13, 2017 |
| Contact name |
chunjiang he |
| E-mail(s) |
camelbbs@163.com
|
| Organization name |
stanford university
|
| Street address |
265 campus drive
|
| City |
stanford |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL16956 |
| Series (1) |
|
