|
| Status |
Public on Apr 11, 2012 |
| Title |
DLD1 5SA-Atoh1-1 |
| Sample type |
RNA |
| |
|
| Source name |
5SA-Atoh1 expressing DLD1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: sporadic colon cancer-derived DLD-1 cells
genotype/variation: Mutated Atoh1 (5SA-Atoh1)
|
| Treatment protocol |
Either GFP or 5SA-Atoh1 was expressed in DLD1 cells by lenti virus infection system.
|
| Growth protocol |
Human sporadic colon cancer-derived DLD-1 cells were cultured in Dubecco’s modified Eagle medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent. All samples showed RNA Integrity Numbers (RIN) more than 9.5.
|
| Label |
Cy3
|
| Label protocol |
RNA samples were labeled using Low Input Quick Amp Labeling Kit (Agilent Technologies). Labeling of 100 ng of total RNA was performed using Cyanine 3-CTP.
|
| |
|
| Hybridization protocol |
Hybridization was carried out using the Gene Expression Hybridization Kit. 1.65 μg of cRNA samples were subjected to fragmentation (30 min at 60°C) and then hybridized on a 4×44K Agilent Whole Human Genome Oligo DNA Microarray Ver2.0 in a rotary oven (10 rpm at 65°C for 17 h).
|
| Scan protocol |
Slides were scanned with Agilent DNA Microarray Scanner.
|
| Data processing |
Gene expression values measured with the microarrays for DLD1_GFP (N=3) and DLD1_5SA-Atoh1 (N=3) were normalized with GeneSpring software by using the 75th percentile value.The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026652_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities.
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| |
|
| Submission date |
Apr 10, 2012 |
| Last update date |
Apr 11, 2012 |
| Contact name |
Kiichiro Tsuchiya |
| Organization name |
Tokyo Medical and Dental University
|
| Street address |
1-5-45 Yushima
|
| City |
Bunkyo-ku |
| ZIP/Postal code |
1138519 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13497 |
| Series (1) |
| GSE37143 |
Gene expression induced by 5SA-Atoh1 in DLD1 cells |
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