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Sample GSM1617917 Query DataSets for GSM1617917
Status Public on Sep 08, 2016
Title H460_shBRG1_GCRA_2
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_GCRA
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_GC_RA_2222
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
Reanalyzed by GSE113533

Data table header descriptions
VALUE Normalized signal intensity

Data table
GE_BrightCorner 16.3641335
DarkCorner 4.072127916
A_23_P117082 12.3986016
A_33_P3246448 12.22913282
A_33_P3318220 4.07764085
A_33_P3236322 5.116110813
A_33_P3319925 5.268487184
A_21_P0000509 18.44872506
A_21_P0000744 10.25953975
A_24_P215804 9.394179643
A_23_P110167 12.40223727
A_33_P3211513 8.669560801
A_23_P103349 5.627305535
A_32_P61480 4.853924802
A_33_P3788124 4.94954625
A_33_P3414202 7.798013801
A_33_P3316686 8.77435212
A_33_P3300975 6.302281994
A_33_P3263061 11.77576917
A_33_P3261373 5.134895258

Total number of rows: 50739

Table truncated, full table size 1257 Kbytes.

Supplementary file Size Download File type/resource
GSM1617917_438_NA_2400253949431285_Cy3_2222_2_4.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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