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Sample GSM2088548 Query DataSets for GSM2088548
Status Public on Mar 15, 2017
Title H1792 trametinib-treated #2
Sample type RNA
Source name H1792 trametinib-treated
Organism Homo sapiens
Characteristics cell line: H1792
origin: lung adenocarcinoma
cell type: Human lung cancer cell line
treated with: 50 nM trametinib for 48 hrs
phenotype: mesenchymal
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 H1792 cells treated with 50 nM trametinib for 48 hours
Data processing The scanned images were analyzed with Feature Extraction Software (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
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
Reanalyzed by GSE113533

Data table header descriptions
VALUE Normalized signal intensity

Data table
GE_BrightCorner 84536.16
DarkCorner 3.6622841
A_23_P117082 17389.502
A_33_P3246448 275.1629
A_33_P3318220 3.7349777
A_33_P3236322 3.7364187
A_33_P3319925 12.168239
A_21_P0000509 51177.73
A_21_P0000744 6341.8193
A_24_P215804 828.2596
A_23_P110167 6326.996
A_33_P3211513 81.33104
A_23_P103349 3.8344576
A_32_P61480 13.641899
A_33_P3788124 3.715316
A_33_P3414202 131.95969
A_33_P3316686 203.09486
A_33_P3300975 123.6713
A_33_P3263061 3652.5474
A_33_P3261373 3.678352

Total number of rows: 50739

Table truncated, full table size 1141 Kbytes.

Supplementary file Size Download File type/resource
GSM2088548_no8_H1792_trametinib_2.txt.gz 12.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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