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Sample GSM2088541 Query DataSets for GSM2088541
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
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 86025.97
DarkCorner 3.6913252
A_23_P117082 2299.5398
A_33_P3246448 3.488439
A_33_P3318220 3.4996912
A_33_P3236322 3.5084867
A_33_P3319925 11.412061
A_21_P0000509 250410.11
A_21_P0000744 788.28937
A_24_P215804 877.1901
A_23_P110167 3885.0732
A_33_P3211513 172.66978
A_23_P103349 3.77687
A_32_P61480 11.866008
A_33_P3788124 3.538245
A_33_P3414202 229.3646
A_33_P3316686 234.43607
A_33_P3300975 3.7791421
A_33_P3263061 3087.3975
A_33_P3261373 3.5199177

Total number of rows: 50739

Table truncated, full table size 1141 Kbytes.

Supplementary file Size Download File type/resource
GSM2088541_no1_H358_parental_1.txt.gz 12.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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