|
| Status |
Public on Jul 26, 2016 |
| Title |
Tumor sample obtained from patient 4 |
| Sample type |
RNA |
| |
|
| Source name |
Tumor sample obtained from patient 4
|
| Organism |
Homo sapiens |
| Characteristics |
cancer status: tumor sample
tissue: stomach
gender: male
|
| Treatment protocol |
All clinical samples were quickly stored in liquid nitrogen after surgical resection.
|
| Growth protocol |
All cancer samples and paired normal samples obtained from GC patients with primary GC from Zhongshan hospital, Fudan University.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cancer cells using TRIzol Reagent (Invitrogen, Shanghai, China), and cDNA was synthesized using a PrimeScript RT reagent kit (Takara, Kusatsu, Shiga, Japan).
|
| Label |
Cy3
|
| Label protocol |
The RNA samples were first reverse transcribed into cDNA, and these cDNA samples were then labeled using a Low Input Quick-Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA).
|
| |
|
| Hybridization protocol |
1.5 ug of Cy3-labelled cDNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Human Gene Expression Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B).
|
| Description |
lncRNA expression
|
| Data processing |
Feature Extraction software (version 10.7.1.1, Agilent Technologies) was used to analyze array images to obtain raw data. GeneSpring software (version 12.5, Agilent Technologies) was employed to finish the basic analysis of the raw data. Initially, the raw data were normalized using the quantile algorithm. The probes with at least 100 percent of samples in any 1 condition out of 2 conditions having flags that indicate “Detected” were chosen for further data analysis. Differentially expressed lncRNAs were then identified through fold change, and p values were calculated using t-tests. The thresholds set for up- and down-regulated genes were a fold change ≥ 2.0 and a p value ≤ 0.05.
|
| |
|
| Submission date |
Jul 25, 2016 |
| Last update date |
Apr 23, 2018 |
| Contact name |
Jianjun Zhang |
| E-mail(s) |
[email protected]
|
| Phone |
86-13817312207
|
| Organization name |
Shanghai Jiaotong University
|
| Street address |
No.639, Zhizaoju road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200011 |
| Country |
China |
| |
|
| Platform ID |
GPL17077 |
| Series (1) |
| GSE84787 |
Human gastric cancer_Tumor samples_Paired normal samples_10 replicates |
|
| Relations |
| Reanalyzed by |
GSE113533 |
