|
| Status |
Public on Mar 15, 2017 |
| Title |
H358 parental #1 |
| Sample type |
RNA |
| |
|
| Source name |
H358 parental
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NCI-H358
origin: lung adenocarcinoma
cell type: Human lung cancer cell line
treated with: PBS for 14 days
phenotype: epihtelial
|
| Treatment protocol |
NCI-H358 parental cells were treated with TGFβ1 (4 ng/mL) or PBS for 14 days in order to induce epithelial to mesenchymal transition (EMT). Induction of EMT was confirmed by western blotting with e-cadherin loss and vimentin expression. For NCI-H1792 experiment, 50 nM trametinib were treated for 48 hours.
|
| Growth protocol |
Cells were cultured in RPMI1640 with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the RNeasy kit (QIAGEN) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-ND1000 spectrophotometer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the one-color Low Input Quick Amp labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes. On completion of the fragmentation reaction, Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE microarray (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven at 10 rpm. 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 by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting (Scan Region 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression of NCI-H358 cells
no1_H358_parental_1.txt
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 039494_D_F_20140813) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Mar 15, 2016 |
| Last update date |
Apr 23, 2018 |
| Contact name |
Hiromichi Ebi |
| E-mail(s) |
hebi@staff.kanazawa-u.ac.jp
|
| Organization name |
Kanazawa University
|
| Department |
Institute for Frontier Science Initiative and Cancer Research Institute
|
| Lab |
Ebi laboratory
|
| Street address |
13-1 Takaramachi
|
| City |
Kanazawa |
| State/province |
Ishikawa |
| ZIP/Postal code |
920-0934 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17077 |
| Series (1) |
| GSE79235 |
Epithelial-to-mesenchymal transition defines feedback activation of receptor tyrosine kinase signaling induced by MEK inhibition in KRAS mutant lung cancer |
|
| Relations |
| Reanalyzed by |
GSE113533 |
