|
| Status |
Public on Dec 31, 2016 |
| Title |
SK-NEP-1_DMSO |
| Sample type |
RNA |
| |
|
| Source name |
SK-NEP-1_DMSO
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SK-NEP-1
cell type: human kidney (Wilm's Tumor) cell line
treated with: DMSO
|
| Treatment protocol |
SK-NEP-1 cells were treated with 2uM SKI-5C and control group cells were treated with the same volume of DMSO 24 hours later.
|
| Growth protocol |
SK-NEP-1 Human kidney (Wilm's Tumor) cell line obtained from the American Type Culture Collection (ATCC) was maintained in the Maccyo’5 (Life Technologies Inc., Gaithersburg, MD, USA) supplemented with 20% heat-inactivated fetal bovine serum (Invitrogen Co., NY, USA) in a humidified incubator with 5% CO2 at 37℃. LBH589 (Cat: S1030 Selleck Chemicals, West Paterson, NJ, USA) was dissolved in DMSO (Cat: D4540 Sigma–Aldrich, St. Louis, MO, USA)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Briefly, RNA purified from total RNA after removal of rRNA was amplified and transcribed into fluorescent cRNA and cDNA was labeled and hybridized to the Human LncRNA Array v3.0 (8660 K, Arraystar). 30,586 LncRNAs and 26,109coding transcripts which collected from the most authoritative databases such as RefSeq, UCSC Knowngenes, Ensembl and many related literatures can be detected by the microarray.
|
| 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)
|
| |
|
| Hybridization protocol |
Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)
|
| Scan protocol |
The hybridized arrays were washed, fixed, and scanned using the Agilent DNA Microarray Scanner (G2505B)
|
| Description |
[Blank](normalized)
|
| Data processing |
Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, lncRNAs and mRNAs that at least 3 out of 15 samples had flagged as “Present” or “Marginal” were chosen for further data analysis. Differentially expressed lncRNAs and mRNAs were identified through fold change (FC) filtering. Differentially expressed lncRNAs and mRNAs with statistical significance (as determined by two-tailed student’s t-test < 0.05) were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). *The Sample data table contains the quantile-normalized intensity from all probes that were detected in at least 3/15 samples prior to any data processing (e.g. prior to fold-change filtering). There was a considerable number of probes not detected in this experiment.
|
| |
|
| Submission date |
Sep 14, 2015 |
| Last update date |
Dec 31, 2016 |
| Contact name |
Jian Pan |
| E-mail(s) |
panjian2008@163.com
|
| Phone |
86-512-67786601
|
| Organization name |
Children's Hospital of Soochow University
|
| Department |
Department of Hematology and Oncology
|
| Street address |
Jingde road 303
|
| City |
suzhou |
| ZIP/Postal code |
215003 |
| Country |
China |
| |
|
| Platform ID |
GPL16956 |
| Series (1) |
|
