|
| Status |
Public on Oct 01, 2010 |
| Title |
HCT116_siCont_24hr |
| Sample type |
RNA |
| |
|
| Source name |
HCT116 cells, siCont, 24hr, replicate 1
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: colorectal cancer
cell line: HCT116
protocol: control
time: 24hr
|
| Treatment protocol |
HCT116 cells pre-transfected with siRNA were stimulated by methyl methanesulfonate (MMS) at 50 ng/ml for 0, 6, 12, and 24 hours.
|
| Growth protocol |
HCT116 cells were cultured in 0.25% FCS for 24 hours, transfected with either control siRNA or siRNA for ATF3 knockdown, and after further 24 hours stimulated with MMS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from MMS-treated HCT116 cells by using Sepasol RNA I Super (nacalai tesque, Japan).
|
| Label |
Cy3
|
| Label protocol |
RNA was labelled with Cy3 according to One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labelling) Ver. 5.7 (Agilent, Japan).
|
| |
|
| Hybridization protocol |
Probes were hybridized to Whole Human Genome Microarray Kit, 4 x 44K according to One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labelling) Ver. 5.7 (Agilent, Japan).
|
| Scan protocol |
Arrays were scanned by Agilent DNA Microarray Scanner using Feature Extraction 9.5.3 (Agilent, Japan).
|
| Description |
Gene expression in HCT116 cells transfected with control siRNA and stimulated with methyl methanesulfonate (MMS) for 24 hr.
|
| Data processing |
Normalization between arrays was done by using average signals of seven house keeping genes (RPS13, RPL27, RPS20, RPL30, RPL13A, RPL9, and SRP14) according to de Jonge HJ et al. Evidence based selection of housekeeping genes. PLoS One. 2007 Sep 19;2(9):e898.
|
| |
|
| Submission date |
Oct 14, 2009 |
| Last update date |
Oct 14, 2009 |
| Contact name |
Yujiro Tanaka |
| E-mail(s) |
yujirotanaka@gmail.com
|
| Organization name |
Tokyo Medical and Dental University
|
| Department |
School of Biomedical Science
|
| Lab |
Genome Structure and Regulation
|
| Street address |
2-3-10 Kandasurugadai
|
| City |
Chiyodaku |
| State/province |
Tokyo |
| ZIP/Postal code |
101-0062 |
| Country |
Japan |
| |
|
| Platform ID |
GPL4133 |
| Series (1) |
| GSE18457 |
ChIP-chip from HCT116 cells treated with MMS and LNCaP cells with ATF3 |
|
