|
| Status |
Public on Jan 07, 2016 |
| Title |
CRC cells-4 DMSO treatment 48 hours |
| Sample type |
RNA |
| |
|
| Source name |
CRC cells, DMSO treatment, 48 hours
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: tumor sample
gender: male
treatment: DMSO treated for 48 hours
|
| Treatment protocol |
CRC cells were treated with DMSO or Aspirin for 48 hours.
|
| Growth protocol |
All CRC cells were cultured in DMEM medium with 10% FBS. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.
|
| 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 after 48 hours in DMSO treated CRC-4 cells
|
| 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 |
Jan 06, 2016 |
| Last update date |
Jan 07, 2016 |
| Contact name |
Jianjun Zhang |
| E-mail(s) |
zjjshuobo@163.com
|
| 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) |
| GSE76583 |
CRC cells_Aspirin treatment_48 hours_Rep8 |
|
