|
| Status |
Public on Sep 30, 2015 |
| Title |
HCT/FR1 FR10 |
| Sample type |
RNA |
| |
|
| Source name |
HCT/FR1 cells with 10ng/ml FR
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: colon cancer cells
cell line: HCT/FR1
|
| Treatment protocol |
Colon cancer cells were seeded at a density of one million cells in P10 plate. The next day, medium was changed to fresh medium with or without 10 ng/ml of FR901464. The cells were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.
|
| Growth protocol |
Colon cancer cell lines were cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIzol and TRIzol RNA Purification kit (Invitrogen) following the manufacture's instructions.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K v2 Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).
|
| Description |
Gene expression with drug treatment
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
|
| |
|
| Submission date |
Jun 05, 2014 |
| Last update date |
Apr 23, 2018 |
| Contact name |
Tomoki Yamano |
| E-mail(s) |
yamanot@hyo-med.ac.jp
|
| Phone |
81-798-45-6371
|
| Organization name |
Hyogo College of Medicine
|
| Department |
Department of Surgery
|
| Lab |
Lower Gastrointestinal Surgery
|
| Street address |
1-1 Mukogawa-cho
|
| City |
Nishinomiya |
| State/province |
Hyogo |
| ZIP/Postal code |
663-8501 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16699 |
| Series (1) |
| GSE58241 |
Gene expression influenced by SF3B1 inhibitor, FR901464 or SF3B1 gene mutations in colorectal cancer cells |
|
| Relations |
| Reanalyzed by |
GSE113533 |
