|
| Status |
Public on Feb 20, 2016 |
| Title |
human colon cancer sw480 cells, control shRNA rep3 [re-analysis] |
| Sample type |
RNA |
| |
|
| Source name |
human colon cancer SW480 cells treated with lentivirus meditated control shRNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SW480
cell type: human colon cancer cell line
transfected with: lentiviral vector GV248 (hU6-MCS-Ubi-EGFP-IRES-Puro) containing negative control
|
| Treatment protocol |
The lentiviral vector GV248 (hU6-MCS-Ubi-EGFP-IRES-Puro) containing YWHAE shRNA hairpin sequence (LV-shYWHAE) and negative control were constructed by Shanghai GeneChem, Transfections were performed using polybrene and enhanced infection solution (Genechem,Shang Hai) according to the manufacturer’s recommended protocol when these cells reached 30% confluence.
|
| Growth protocol |
The human colon cancer cell lines SW480 cells were cultured in DMEM medium(Gibco BRL Co.Ltd.,USA) supplemented with 100 ml/l FBS (Gibco,USA) with the addition of 100 U/ml penicillin and 100 U/ml streptomycin at 37C in a humidified atmosphere of5 % CO2 in air.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
|
| Label |
biotin
|
| Label protocol |
Synthesis of cDNA and subsequent biotin labeling of cRNA was performed according to the manufacturer´s protocol (GeneChip 3’IVT Express Kit; Affymetrix, Inc.). Briefly, 200 ng of total RNA were converted to cDNA, followed by in vitro transcription and biotin labeling of aRNA
|
| |
|
| Hybridization protocol |
After fragmentation labeled aRNA was hybridized to Affymetrix PrimeView Human Gene Expression Microarrays for 16h at 45 °C, stained by strepatavidin/phycoerythrin conjugate and scanned as described in the manufacturer´s protocol
|
| Scan protocol |
Gene ChIP Scanner 3000 7G (Affymetrix Inc.); AGCC (Vers. 3.3)
|
| Description |
3683-3_(PrimeView)
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Partek® Genomics SuiteTM. Expression values were RMA normalized, and fold-change values were then calculated using least-squares mean between samples.
|
| |
|
| Submission date |
Feb 19, 2016 |
| Last update date |
Feb 20, 2016 |
| Contact name |
Yousheng Huang |
| E-mail(s) |
hys768811@163.com
|
| Organization name |
Hainan Medical university
|
| Department |
Department of pathology
|
| Street address |
The 3rd Xueyuan Road
|
| City |
Haikou |
| State/province |
Hainan |
| ZIP/Postal code |
570102 |
| Country |
China |
| |
|
| Platform ID |
GPL15207 |
| Series (1) |
| GSE78094 |
Silcening YWHAE gene expression suppresses the proliferation of colon cancer cells by inducing gene differentially expressed. |
|
| Relations |
| Reanalysis of |
GSM2066591 |
