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Sample GSM1617915 Query DataSets for GSM1617915
Status Public on Sep 08, 2016
Title H460_shBRG1_FBS_3
Sample type RNA
 
Source name Lung
Organism Homo sapiens
Characteristics individual: Diseased donor
cell line: NSCLC cell line H460
cell line type: MYC amplified
treatment: shBRG1_FBS
Treatment protocol GCRA: Dexamethasone (1uM) + Retinoic Acid (1uM) 120hours; COMB: Dexamethasone (1uM) + Retinoic Acid (1uM) + Aza (0.2uM) + SAHA (0.2uM) 120 hours
Growth protocol Cells where growth on RPMI media with 10% FBS, 1% PS
Extracted molecule total RNA
Extraction protocol Total RNA were extracted using Trizol Reagent.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 45ng total RNA using a LowInput QuickAmp Labeling Kit (Agilent Technologies, Palo Alto, Calif, USA) 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 (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a total volume of 25ul following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. 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 Scanner Agilent G2565CA Feature extraction 10.7
Description Sample name: H460_Sh_FBS_2213
Cancer cell line
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Feb 24, 2015
Last update date Apr 23, 2018
Contact name Manel Esteller
Organization name IDIBELL
Department PEBC
Lab Cancer Epigenetics
Street address Hospital Duran i Reynals Av. Gran Via s/n km, 2.7
City L'Hospitalet de Llobregat
State/province Barcelona
ZIP/Postal code 08908
Country Spain
 
Platform ID GPL17077
Series (2)
GSE66244 Identification of expresion patterns after treatment with GC/RA and combination with AZA/SAHA in MYC amplified and BRG1 mutant lung cancer cell lines
GSE66245 Treatment with GC/RA and combination with AZA/SAHA in MYC amplified and BRG1 mutant lung cancer cell lines
Relations
Reanalyzed by GSE113533

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
GE_BrightCorner 16.18311038
DarkCorner 4.251459746
A_23_P117082 12.3431938
A_33_P3246448 12.40187094
A_33_P3318220 5.598825715
A_33_P3236322 5.122147899
A_33_P3319925 5.358668026
A_21_P0000509 18.32014492
A_21_P0000744 10.58163693
A_24_P215804 9.138759955
A_23_P110167 12.02889996
A_33_P3211513 8.372112241
A_23_P103349 5.994874402
A_32_P61480 4.921693604
A_33_P3788124 4.240125057
A_33_P3414202 7.834527188
A_33_P3316686 8.769656861
A_33_P3300975 5.407997644
A_33_P3263061 10.69496704
A_33_P3261373 4.860260274

Total number of rows: 50739

Table truncated, full table size 1259 Kbytes.




Supplementary file Size Download File type/resource
GSM1617915_436_NA_2100253949431326_Cy3_2213_2_1.txt.gz 12.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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