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Sample GSM2088542 Query DataSets for GSM2088542
Status Public on Mar 15, 2017
Title H358 parental #2
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
no2_H358_parental_2.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

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
GE_BrightCorner 89008.66
DarkCorner 3.0884209
A_23_P117082 3490.4712
A_33_P3246448 5.2524686
A_33_P3318220 3.178753
A_33_P3236322 8.31386
A_33_P3319925 11.742899
A_21_P0000509 297904.06
A_21_P0000744 807.6221
A_24_P215804 1011.0963
A_23_P110167 3633.7485
A_33_P3211513 150.77608
A_23_P103349 5.0988193
A_32_P61480 19.619276
A_33_P3788124 3.1878352
A_33_P3414202 266.40088
A_33_P3316686 285.14197
A_33_P3300975 3.1750488
A_33_P3263061 1926.2931
A_33_P3261373 3.1637518

Total number of rows: 50739

Table truncated, full table size 1139 Kbytes.




Supplementary file Size Download File type/resource
GSM2088542_no2_H358_parental_2.txt.gz 12.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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