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Sample GSM1715603 Query DataSets for GSM1715603
Status Public on Sep 08, 2016
Title H1299_GCRA_3
Sample type RNA
Source name Non Small Cell Lung Cancer (NSCLC)
Organism Homo sapiens
Characteristics individual: Diseased donor
cell line: H1299
cell line type: BRG1 mutant
treatment: 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: 042_MA__1400253949437761__Cy3_413_1_4
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 Jun 18, 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 16.54359802
DarkCorner 5.235306552
A_23_P117082 13.63019119
A_33_P3246448 5.278649442
A_33_P3318220 5.121759642
A_33_P3236322 5.576120474
A_33_P3319925 5.633755393
A_21_P0000509 17.51510679
A_21_P0000744 12.89062023
A_24_P215804 10.21679439
A_23_P110167 4.895760148
A_33_P3211513 8.553463033
A_23_P103349 4.967100065
A_32_P61480 5.925103548
A_33_P3788124 5.121759642
A_33_P3414202 7.919598505
A_33_P3316686 9.662591299
A_33_P3300975 11.15412263
A_33_P3263061 12.35190116
A_33_P3261373 5.500237387

Total number of rows: 50739

Table truncated, full table size 1259 Kbytes.

Supplementary file Size Download File type/resource
GSM1715603_042_MA_1400253949437761_Cy3_413_1_4.txt.gz 12.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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