|
| Status |
Public on Jan 20, 2017 |
| Title |
HCT116_24h_DMSO_replicate_3 |
| Sample type |
RNA |
| |
|
| Source name |
HCT116_24h_DMSO_replicate_3
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: cultured cell
cell line: HCT116
|
| Treatment protocol |
HCT116 cells were seeded in a six-well plate at a density of 1.0 × 105 cells per well with or without the siRNA reverse transfection of the siGENOME SMARTpool of RBM39 (Dharmacon, M-011965) and non-targeting siRNA pool #2 (D-001206-14). Following incubation overnight, DMSO or E7820 were added to the siRNA-free HCT116 plate (final 1 μM of E7820) and incubated for 24 hours.
|
| Growth protocol |
Cells were cultured in RPMI-1640 (Wako) supplemented with 10% fetal bovine serum (FBS; Sigma Aldrich) and 1% penicillin-streptomycin (Wako), and grown at 37 °C in a humidified incubator under 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using RNeasy mini spin columns (Qiagen), according to the manufacturer’s protocol. The yield and quality of each isolated total RNA sample was determined using a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific) and an RNA Nano LabChip(R) kit analyzed on a 2100 Bioanalyzer (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
Total RNA (200 ng) was converted to cyanine-3 (Cy3)-labeled complementary RNA (cRNA) using a Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies), according to the manufacturer’s instructions for single-color 8×60K gene expression arrays. Cy3-labeled cRNAs were purified using an RNeasy Mini purification kit (Qiagen).
|
| |
|
| Hybridization protocol |
Cy3-labeled cRNAs were hybridized to the SurePrint G3 Human Gene Expression 8×60K Microarray (Agilent Technologies) at 65 °C for 17 hours with a Gene Expression Hybridization Kit (Agilent Technologies), according to the manufacturer’s instructions. The arrays were washed with a Gene Expression Wash Pack (Agilent Technologies), according to the manufacturer’s instructions.
|
| Scan protocol |
Slides were scanned on a DNA Microarray Scanner (Agilent Technologies), according to the manufacturer’s instructions.
|
| Description |
Gene expression after 24hr treatment with DMSO
|
| Data processing |
The scanned images were then quantified using Feature Extraction software (version 11.5.1.1, Agilent Technologies), and the resulting files were imported and analyzed with GeneSpring (version 12.5, Agilent Technologies).
|
| |
|
| Submission date |
Jan 19, 2017 |
| Last update date |
Apr 23, 2018 |
| Contact name |
Taisuke Uehara |
| Organization name |
Eisai Co., Ltd.
|
| Department |
Oncology Business Group
|
| Lab |
EWAY
|
| Street address |
Tokodai 5-1-3
|
| City |
Tsukuba-shi |
| State/province |
Ibaraki |
| ZIP/Postal code |
300-2635 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17077 |
| Series (1) |
| GSE93829 |
Selective Degradation of Splicing Factor CAPER-alpha by Anticancer Sulfonamides |
|
| Relations |
| Reanalyzed by |
GSE113533 |
