|
| Status |
Public on May 14, 2007 |
| Title |
DLD-1 cell line treated with 5-aza-2’-deoxycytidine |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
DLD-1 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
DLD-1 cell line is derived from colorectal adenocarcinoma (Dukes' type C).
|
| Growth protocol |
DLD-1 cell line was maintained in RPMI1640. It was supplemented with 10% fetal bovine serum and was cultured under 5% CO2 at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TriZol procedure
|
| Label |
Cy3
|
| Label protocol |
Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp™ aRNA Amplification Kit (Ambion). CyeDye Coupling and fragmentation were performed as the protocol supplied by Hitach Software Engineering Co., Ltd. Detailed protocols at the DNA Chip Research Inc. website.
|
| |
|
| Channel 2 |
| Source name |
DLD-1 cell line treated with 5-aza-2’-deoxycytidine
|
| Organism |
Homo sapiens |
| Characteristics |
DLD-1 cell line is derived from colorectal adenocarcinoma (Dukes' type C).
|
| Treatment protocol |
For demethylation experiments, cells were plated at a density of 2×105 cells/75 cm2 flask and cultured for 24 h, followed by 96 h incubation with 1 μM 5-aza-2’-deoxycytidine (Sigma Chemical Co., St. Louis, MO).
|
| Growth protocol |
DLD-1 cell line was maintained in RPMI1640. It was supplemented with 10% fetal bovine serum and was cultured under 5% CO2 at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TriZol procedure
|
| Label |
Cy5
|
| Label protocol |
Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp™ aRNA Amplification Kit (Ambion). CyeDye Coupling and fragmentation were performed as the protocol supplied by Hitach Software Engineering Co., Ltd. Detailed protocols at the DNA Chip Research Inc. website.
|
| |
|
| |
| Hybridization protocol |
Hybridized for 16 h at 42 C. Hybridization buffer and washing protocol was followed by the protocol supplied by Hitach Software Engineering Co., Ltd. Detailed protocols at the DNA Chip Research Inc. website.
|
| Scan protocol |
ScanArray HT (PerkinElmer Japan Co., Ltd.) was used for scanning. Array images were analyzed with DNASIS Array (Hitachi Software Engineering Co., Ltd.).
|
| Description |
DLD1
|
| Data processing |
This data were analyzed by DNASIS array software(Hitachi Software Engineering), which converted the signal intensity of each spot into text format. Log2-ratios of the median subtracted background intensity levels were analyzed. Data from each microarray were normalized by LOWESS normalization.
|
| |
|
| Submission date |
May 02, 2007 |
| Last update date |
May 14, 2007 |
| Contact name |
Satoshi Fukutomi |
| E-mail(s) |
satoshifukutomi@yahoo.co.jp
|
| Organization name |
Chiba University
|
| Department |
General Surgery
|
| Street address |
1-8-1 Inohana Chuoku
|
| City |
Chiba |
| ZIP/Postal code |
260-8677 |
| Country |
Japan |
| |
|
| Platform ID |
GPL1291 |
| Series (1) |
| GSE7687 |
Methylation-silenced genes in colorectal cancer cell lines |
|
