|
| Status |
Public on Dec 11, 2008 |
| Title |
SW48 p53 WT HETEROZYGOUS Colorectal cancer cells_12 Gy gamma radiation |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
SW48 Colorectal cancer cell line, exposed to 12Gy gamma radiation and incubated 24 hours before sample collection
|
| Organism |
Homo sapiens |
| Characteristics |
Cell Line: SW48, p53 status: +/-, Treatment: 12 Gy gamma radiation
|
| Treatment protocol |
Exposure to 12 Gy gamma radiation
|
| Growth protocol |
Cells grown to 70% confluence in T75 flasks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Qiagen RNeasy Plant kit according to manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
cDNA was used as a template for in vitro transcription using T7 RNA polymerase and Cy-3 and Cy-5 labeled CTP
|
| |
|
| Channel 2 |
| Source name |
SW48 Colorectal cancer cell line, nonirradiated and incubated for same time as irradiated samples
|
| Organism |
Homo sapiens |
| Characteristics |
Cell Line: SW48, p53 status: +/-, Treatment: No radiation
|
| Treatment protocol |
Exposure to 12 Gy gamma radiation
|
| Growth protocol |
Cells grown to 70% confluence in T75 flasks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Qiagen RNeasy Plant kit according to manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
cDNA was used as a template for in vitro transcription using T7 RNA polymerase and Cy-3 and Cy-5 labeled CTP
|
| |
|
| |
| Hybridization protocol |
Samples from the same cell line with and without gamma irradiation were hybridized to the same slide. Labeled cRNA samples were used for hybridization to Agilent 4x44K microarrays and scanned as directed by the manufacurer.
|
| Scan protocol |
Agilent microarray scanner,as according to manufacturer
|
| Description |
colorectal cancer cell lines that differ only with respect to their endogenous TP53 status
|
| Data processing |
Data were extracted using Feature Extraction software v8.1 (Agilent Technologies) under default settings for normalization. Microarrays with higher than 5 percent feature of local background region outliers were excluded. Distributions of signal and background intensity of both red and green channels were examined with boxplot and maPlot using the Bioconductor package. The ratios of each feature were calculated after background subtraction and normalization. Features exhibiting signifcant changes of gene expression were selected based on PValueLogRatio calculated from the feature extraction software.
|
| |
|
| Submission date |
Dec 09, 2008 |
| Last update date |
Dec 11, 2008 |
| Contact name |
Raymond Anthony Pagliarini |
| Organization name |
NIBRI
|
| Department |
Oncology
|
| Street address |
250 Massachusetts Ave. Room 3C-292
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL4133 |
| Series (1) |
| GSE13886 |
Response of p53 isogenic colorectal cancer panel to 12 Gy gamma irradiation |
|
